#include <connection_manager.h>

Inheritance diagram for nest::ConnectionManager:

Collaboration diagram for nest::ConnectionManager:

Public Types
enum	ConnectionType { CONNECT , CONNECT_FROM_DEVICE , CONNECT_TO_DEVICE , NO_CONNECTION }

Public Member Functions
	ConnectionManager ()

	~ConnectionManager () override

void	initialize (const bool) override
	Prepare manager for operation.

void	finalize (const bool) override
	Take down manager after operation.

void	set_status (const Dictionary &) override
	Set the status of the manager.

void	get_status (Dictionary &) override
	Retrieve the status of the manager.

bool	valid_connection_rule (std::string)

void	compute_target_data_buffer_size ()

void	compute_compressed_secondary_recv_buffer_positions (const size_t tid)

void	collect_compressed_spike_data (const size_t tid)

void	clear_compressed_spike_data_map ()

template<typename ConnBuilder >
void	register_conn_builder (const std::string &name)
	Add a connectivity rule, i.e.

template<typename ThirdConnBuilder >
void	register_third_conn_builder (const std::string &name)
	Add a connectivity rule, i.e.

BipartiteConnBuilder *	get_conn_builder (const std::string &name, NodeCollectionPTR sources, NodeCollectionPTR targets, ThirdOutBuilder *third_out, const Dictionary &conn_spec, const std::vector< Dictionary > &syn_specs)
	Obtain builder for bipartite connections.

ThirdOutBuilder *	get_third_conn_builder (const std::string &name, NodeCollectionPTR sources, NodeCollectionPTR targets, ThirdInBuilder *third_in, const Dictionary &conn_spec, const std::vector< Dictionary > &syn_specs)
	Obtain builder for bipartite connections.

void	connect (NodeCollectionPTR sources, NodeCollectionPTR targets, const Dictionary &conn_spec, const std::vector< Dictionary > &syn_specs)
	Create connections.

void	connect (const size_t snode_id, Node *target, size_t target_thread, const synindex syn_id, const Dictionary &params, const double delay=numerics::nan, const double weight=numerics::nan)
	Connect two nodes.

bool	connect (const size_t snode_id, const size_t target, const Dictionary &params, const synindex syn_id)
	Connect two nodes.

void	connect_arrays (const long sources, const long targets, const double weights, const double delays, const std::vector< std::string > &p_keys, const double *p_values, size_t n, const std::string &syn_model)

void	connect_sonata (const Dictionary &graph_specs, const long hyberslab_size)
	Connect nodes from SONATA specification.

void	connect_tripartite (NodeCollectionPTR sources, NodeCollectionPTR targets, NodeCollectionPTR third, const Dictionary &connectivity, const Dictionary &third_connectivity, const std::map< std::string, std::vector< Dictionary > > &synapse_specs)
	Create tripartite connections.

size_t	find_connection (const size_t tid, const synindex syn_id, const size_t snode_id, const size_t tnode_id)
	Find first non-disabled thread-local connection of given synapse type with given source and target node.

void	disconnect (const size_t tid, const synindex syn_id, const size_t snode_id, const size_t tnode_id)

ConnectionType	connection_required (Node &source, Node &target, size_t tid)
	Check whether a connection between the given source and target nodes can be established on the given thread with id tid.

Dictionary	get_synapse_status (const size_t source_node_id, const size_t target_node_id, const size_t tid, const synindex syn_id, const size_t lcid) const

void	set_synapse_status (const size_t source_node_id, const size_t target_node_id, const size_t tid, const synindex syn_id, const size_t lcid, const Dictionary &dict)

std::deque< ConnectionID >	get_connections (const Dictionary &params)
	Return connections between pairs of neurons.

void	get_connections (std::deque< ConnectionID > &connectome, NodeCollectionPTR source, NodeCollectionPTR target, synindex syn_id, long synapse_label) const

size_t	get_num_connections () const
	Returns the number of connections in the network.

size_t	get_num_connections (const synindex syn_id) const
	Returns the number of connections of this synapse type.

void	get_sources (const std::vector< size_t > &targets, const size_t syn_id, std::vector< std::vector< size_t > > &sources)

void	get_targets (const std::vector< size_t > &sources, const size_t syn_id, const std::string &post_synaptic_element, std::vector< std::vector< size_t > > &targets)

const std::vector< Target > &	get_remote_targets_of_local_node (const size_t tid, const size_t lid) const

size_t	get_target_node_id (const size_t tid, const synindex syn_id, const size_t lcid) const

bool	get_device_connected (size_t tid, size_t lcid) const

void	trigger_update_weight (const long vt_node_id, const std::vector< spikecounter > &dopa_spikes, const double t_trig)
	Triggered by volume transmitter in update.

long	get_min_delay () const
	Return minimal connection delay, which is precomputed by update_delay_extrema_().

long	get_max_delay () const
	Return maximal connection delay, which is precomputed by update_delay_extrema_().

bool	get_user_set_delay_extrema () const

void	send (const size_t tid, const synindex syn_id, const size_t lcid, const std::vector< ConnectorModel * > &cm, Event &e)

void	send_to_devices (const size_t tid, const size_t source_node_id, Event &e)
	Send event e to all device targets of source source_node_id.

void	send_to_devices (const size_t tid, const size_t source_node_id, SecondaryEvent &e)

void	send_from_device (const size_t tid, const size_t ldid, Event &e)
	Send event e to all targets of source device ldid (local device id)

void	send_local (size_t t, Node &source, Event &e)
	Send event e to all targets of node source on thread t.

void	calibrate (const TimeConverter &)
	Resize the structures for the Connector objects if necessary.

DelayChecker &	get_delay_checker ()
	Returns the delay checker for the current thread.

void	clean_source_table (const size_t tid)
	Removes processed entries from source table.

void	clear_source_table (const size_t tid)
	Clears all entries in source table.

bool	get_keep_source_table () const
	Returns true if source table is kept after building network.

bool	is_source_table_cleared () const
	Returns true if source table was cleared.

void	prepare_target_table (const size_t tid)

void	resize_target_table_devices_to_number_of_neurons ()

void	resize_target_table_devices_to_number_of_synapse_types ()

bool	get_next_target_data (const size_t tid, const size_t rank_start, const size_t rank_end, size_t &target_rank, TargetData &next_target_data)

bool	fill_target_buffer (const size_t tid, const size_t rank_start, const size_t rank_end, std::vector< TargetData > &send_buffer_target_data, TargetSendBufferPosition &send_buffer_position)

void	reject_last_target_data (const size_t tid)

void	save_source_table_entry_point (const size_t tid)

void	reset_source_table_entry_point (const size_t tid)

void	restore_source_table_entry_point (const size_t tid)

void	add_target (const size_t tid, const size_t target_rank, const TargetData &target_data)

bool	use_compressed_spikes () const
	Returns whether spikes should be compressed.

void	sort_connections (const size_t tid)
	Sorts connections in the presynaptic infrastructure by increasing source node ID.

bool	connections_have_changed () const
	Returns true if connection information needs to be communicated.

void	set_connections_have_changed ()
	Sets flag indicating whether connection information needs to be communicated to true.

void	unset_connections_have_changed ()
	Sets flag indicating whether connection information needs to be communicated to false.

void	restructure_connection_tables (const size_t tid)
	Deletes TargetTable and resets processed flags of SourceTable.

void	set_source_has_more_targets (const size_t tid, const synindex syn_id, const size_t lcid, const bool more_targets)

void	no_targets_to_process (const size_t tid)

const std::vector< size_t > &	get_secondary_send_buffer_positions (const size_t tid, const size_t lid, const synindex syn_id) const

size_t	get_secondary_recv_buffer_position (const size_t tid, const synindex syn_id, const size_t lcid) const
	Returns read position in MPI receive buffer for secondary connections.

bool	deliver_secondary_events (const size_t tid, const bool called_from_wfr_update, std::vector< unsigned int > &recv_buffer)

void	compress_secondary_send_buffer_pos (const size_t tid)

void	resize_connections ()

void	sync_has_primary_connections ()

void	check_secondary_connections_exist ()

bool	has_primary_connections () const

bool	secondary_connections_exist () const

size_t	get_source_node_id (const size_t tid, const synindex syn_id, const size_t lcid)

double	get_stdp_eps () const

void	set_stdp_eps (const double stdp_eps)

const std::vector< SpikeData > &	get_compressed_spike_data (const synindex syn_id, const size_t idx)

void	initialize_iteration_state ()
	Set iteration_state_ entries for all threads to beginning of compressed_spike_data_map_.

Public Member Functions inherited from nest::ManagerInterface
	ManagerInterface (ManagerInterface const &)=delete

void	operator= (ManagerInterface const &)=delete

	ManagerInterface ()

virtual	~ManagerInterface ()

virtual void	prepare ()

virtual void	cleanup ()

Public Attributes
Stopwatch< StopwatchGranularity::Normal, StopwatchParallelism::MasterOnly >	sw_construction_connect

Private Member Functions
size_t	get_num_target_data (const size_t tid) const

size_t	get_num_connections_ (const size_t tid, const synindex syn_id) const

void	get_connections_ (const size_t tid, std::deque< ConnectionID > &connectome, NodeCollectionPTR source, NodeCollectionPTR target, synindex syn_id, long synapse_label) const
	See get_connections()

void	get_connections_to_targets_ (const size_t tid, std::deque< ConnectionID > &connectome, NodeCollectionPTR source, NodeCollectionPTR target, synindex syn_id, long synapse_label) const

void	get_connections_from_sources_ (const size_t tid, std::deque< ConnectionID > &connectome, NodeCollectionPTR source, NodeCollectionPTR target, synindex syn_id, long synapse_label) const

void	get_source_node_ids_ (const size_t tid, const synindex syn_id, const size_t tnode_id, std::vector< size_t > &sources)

void	remove_disabled_connections_ (const size_t tid)
	Removes disabled connections (of structural plasticity)

void	split_to_neuron_device_vectors_ (const size_t tid, NodeCollectionPTR nodecollection, std::vector< size_t > &neuron_node_ids, std::vector< size_t > &device_node_ids) const
	Splits a TokenArray of node IDs to two vectors containing node IDs of neurons and node IDs of devices.

void	update_delay_extrema_ ()
	Update delay extrema to current values.

const Time	get_min_delay_time_ () const
	This method queries and finds the minimum delay of all local connections.

const Time	get_max_delay_time_ () const
	This method queries and finds the maximum delay of all local connections.

void	delete_connections_ ()
	Deletes all connections.

void	connect_ (Node &source, Node &target, const size_t s_node_id, const size_t tid, const synindex syn_id, const Dictionary &params, const double delay=numerics::nan, const double weight=numerics::nan)
	connect_ is used to establish a connection between a sender and receiving node which both have proxies.

void	connect_to_device_ (Node &source, Node &target, const size_t s_node_id, const size_t tid, const synindex syn_id, const Dictionary &params, const double delay=NAN, const double weight=NAN)
	connect_to_device_ is used to establish a connection between a sender and receiving node if the sender has proxies, and the receiver does not.

void	connect_from_device_ (Node &source, Node &target, const size_t tid, const synindex syn_id, const Dictionary &params, const double delay=NAN, const double weight=NAN)
	connect_from_device_ is used to establish a connection between a sender and receiving node if the sender does not have proxies.

void	increase_connection_count (const size_t tid, const synindex syn_id)
	Increases the connection count.

Private Attributes
std::vector< std::vector< ConnectorBase * > >	connections_
	A structure to hold the Connector objects which in turn hold the connection information.

SourceTable	source_table_
	A structure to hold the node IDs of presynaptic neurons during postsynaptic connection creation, before the connection information has been transferred to the presynaptic side.

std::vector< std::vector< std::vector< SpikeData > > >	compressed_spike_data_
	A structure to hold "unpacked" spikes on the postsynaptic side if spike compression is enabled.

std::vector< std::vector< std::vector< size_t > > >	secondary_recv_buffer_pos_
	Stores absolute position in receive buffer of secondary events.

std::map< size_t, size_t >	buffer_pos_of_source_node_id_syn_id_

TargetTable	target_table_
	A structure to hold the information about targets for each neuron on the presynaptic side.

TargetTableDevices	target_table_devices_

std::vector< DelayChecker >	delay_checkers_

std::vector< std::vector< size_t > >	num_connections_
	A structure to count the number of synapses of a specific type.

Dictionary	connruledict_
	Dictionary for connection rules.

std::vector< GenericBipartiteConnBuilderFactory * >	connbuilder_factories_
	ConnBuilder factories, indexed by connruledict_ elements.

Dictionary	thirdconnruledict_
	Dictionary for third-factor connection rules.

std::vector< GenericThirdConnBuilderFactory * >	thirdconnbuilder_factories_
	Third-factor ConnBuilder factories, indexed by thirdconnruledict_ elements.

long	min_delay_
	Value of the smallest delay in the network.

long	max_delay_
	Value of the largest delay in the network in steps.

bool	keep_source_table_
	Whether to keep source table after connection setup is complete.

bool	connections_have_changed_
	True if new connections have been created since startup or last call to simulate.

bool	get_connections_has_been_called_
	true if GetConnections has been called.

bool	use_compressed_spikes_
	Whether to use spike compression; if a neuron has targets on multiple threads of a process, this switch makes sure that only a single packet is sent to the process instead of one packet per target thread; implies sort_connections_by_source_ = true; for more details see the discussion and sketch in https://github.com/nest/nest-simulator/pull/1338.

bool	has_primary_connections_
	Whether primary connections (spikes) exist.

PerThreadBoolIndicator	check_primary_connections_
	Check for primary connections (spikes) on each thread.

bool	secondary_connections_exist_
	Whether secondary connections (e.g., gap junctions) exist.

PerThreadBoolIndicator	check_secondary_connections_
	Check for secondary connections (e.g., gap junctions) on each thread.

double	stdp_eps_
	Maximum distance between (double) spike times in STDP that is still considered 0.

std::vector< std::pair< size_t, std::map< size_t, CSDMapEntry >::const_iterator > >	iteration_state_
	For each thread, store (syn_id, compressed_spike_data_map_::iterator) pair for next iteration while filling target buffers.

Friends
class	SimulationManager

Member Enumeration Documentation

◆ ConnectionType

enum nest::ConnectionManager::ConnectionType

Enumerator
CONNECT
CONNECT_FROM_DEVICE
CONNECT_TO_DEVICE
NO_CONNECTION

Constructor & Destructor Documentation

◆ ConnectionManager()

nest::ConnectionManager::ConnectionManager ( )

◆ ~ConnectionManager()

nest::ConnectionManager::~ConnectionManager ( )

override

Member Function Documentation

◆ add_target()

void nest::ConnectionManager::add_target	(	const size_t	tid,
		const size_t	target_rank,
		const TargetData &	target_data
	)

inline

References nest::TargetTable::add_target(), and target_table_.

Referenced by nest::EventDeliveryManager::distribute_target_data_buffers_().

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◆ calibrate()

void nest::ConnectionManager::calibrate ( const TimeConverter & tc )

Resize the structures for the Connector objects if necessary.

This function should be called after number of threads, min_delay, max_delay, and time representation have been changed in the scheduler. The TimeConverter is used to convert times from the old to the new representation. It is also forwarding the calibration request to all ConnectorModel objects.

References delay_checkers_, nest::VPManager::get_num_threads(), nest::kernel(), and nest::KernelManager::vp_manager.

Referenced by nest::SimulationManager::set_status().

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◆ check_secondary_connections_exist()

void nest::ConnectionManager::check_secondary_connections_exist ( )

References nest::MPIManager::any_true(), nest::kernel(), nest::KernelManager::mpi_manager, and secondary_connections_exist_.

Referenced by nest::SimulationManager::update_connection_infrastructure().

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◆ clean_source_table()

void nest::ConnectionManager::clean_source_table ( const size_t tid )

inline

Removes processed entries from source table.

References nest::SourceTable::clean(), keep_source_table_, and source_table_.

Referenced by nest::EventDeliveryManager::gather_target_data().

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◆ clear_compressed_spike_data_map()

void nest::ConnectionManager::clear_compressed_spike_data_map ( )

inline

References nest::SourceTable::clear_compressed_spike_data_map(), and source_table_.

Referenced by nest::SimulationManager::update_connection_infrastructure().

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◆ clear_source_table()

void nest::ConnectionManager::clear_source_table ( const size_t tid )

inline

Clears all entries in source table.

References nest::SourceTable::clear(), keep_source_table_, and source_table_.

Referenced by nest::EventDeliveryManager::gather_target_data(), and nest::EventDeliveryManager::gather_target_data_compressed().

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◆ collect_compressed_spike_data()

void nest::ConnectionManager::collect_compressed_spike_data ( const size_t tid )

References nest::SourceTable::collect_compressible_sources(), compressed_spike_data_, nest::SourceTable::fill_compressed_spike_data(), nest::KernelManager::get_omp_synchronization_construction_stopwatch(), nest::kernel(), nest::SourceTable::resize_compressible_sources(), source_table_, nest::Stopwatch< detailed_timer, threaded_timer >::start(), nest::Stopwatch< detailed_timer, threaded_timer >::stop(), and use_compressed_spikes_.

Referenced by nest::SimulationManager::update_connection_infrastructure().

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◆ compress_secondary_send_buffer_pos()

void nest::ConnectionManager::compress_secondary_send_buffer_pos ( const size_t tid )

References nest::TargetTable::compress_secondary_send_buffer_pos(), and target_table_.

Referenced by nest::SimulationManager::update_connection_infrastructure().

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◆ compute_compressed_secondary_recv_buffer_positions()

void nest::ConnectionManager::compute_compressed_secondary_recv_buffer_positions ( const size_t tid )

References buffer_pos_of_source_node_id_syn_id_, nest::SourceTable::compute_buffer_pos_for_unique_secondary_sources(), connections_, nest::ModelManager::get_connection_model(), nest::SourceTable::get_node_id(), get_num_connections_(), nest::MPIManager::get_process_id_of_node_id(), nest::MPIManager::get_recv_displacement_secondary_events_in_int(), nest::ConnectorModel::has_property(), nest::IS_PRIMARY, nest::kernel(), nest::KernelManager::model_manager, nest::KernelManager::mpi_manager, nest::SourceTable::pack_source_node_id_and_syn_id(), secondary_recv_buffer_pos_, and source_table_.

Referenced by nest::SimulationManager::update_connection_infrastructure().

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◆ compute_target_data_buffer_size()

void nest::ConnectionManager::compute_target_data_buffer_size ( )

References nest::MPIManager::communicate(), nest::MPIManager::get_num_processes(), get_num_target_data(), nest::VPManager::get_num_threads(), nest::MPIManager::get_rank(), nest::kernel(), nest::KernelManager::mpi_manager, nest::MPIManager::set_buffer_size_target_data(), and nest::KernelManager::vp_manager.

Referenced by nest::SimulationManager::update_connection_infrastructure().

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◆ connect() [1/3]

bool nest::ConnectionManager::connect	(	const size_t	snode_id,
		const size_t	target,
		const Dictionary &	params,
		const synindex	syn_id
	)

Connect two nodes.

The source and target nodes are defined by their global ID. The connection is established on the thread/process that owns the target node.

Parameters

snode_id	node ID of the sending Node.
target	node ID of the target Node.
params	Parameter dictionary to configure the synapse.
syn_id	The synapse model to use.

References nest::ModelManager::assert_valid_syn_id(), CONNECT, connect_(), CONNECT_FROM_DEVICE, connect_from_device_(), CONNECT_TO_DEVICE, connect_to_device_(), connection_required(), nest::NodeManager::get_node_or_proxy(), nest::VPManager::get_thread_id(), nest::kernel(), nest::KernelManager::model_manager, NO_CONNECTION, nest::KernelManager::node_manager, and nest::KernelManager::vp_manager.

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◆ connect() [2/3]

void nest::ConnectionManager::connect	(	const size_t	snode_id,
		Node *	target,
		size_t	target_thread,
		const synindex	syn_id,
		const Dictionary &	params,
		const double	delay = `numerics::nan`,
		const double	weight = `numerics::nan`
	)

Connect two nodes.

The source node is defined by its global ID. The target node is defined by the node. The connection is established on the thread/process that owns the target node.

The parameters delay and weight have the default value numerics::nan. numerics::nan is a special value, which describes double values that are not a number. If delay or weight is omitted in a connect call, numerics::nan indicates this and weight/delay are set only, if they are valid.

Parameters

snode_id	node ID of the sending Node.
target	Pointer to target Node.
target_thread	Thread that hosts the target node.
syn_id	The synapse model to use.
params	Parameter dictionary to configure the synapse.
delay	Delay of the connection (in ms).
weight	Weight of the connection.

References nest::ModelManager::assert_valid_syn_id(), CONNECT, connect_(), CONNECT_FROM_DEVICE, connect_from_device_(), CONNECT_TO_DEVICE, connect_to_device_(), connection_required(), nest::NodeManager::get_node_or_proxy(), nest::kernel(), nest::KernelManager::model_manager, NO_CONNECTION, and nest::KernelManager::node_manager.

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◆ connect() [3/3]

void nest::ConnectionManager::connect	(	NodeCollectionPTR	sources,
		NodeCollectionPTR	targets,
		const Dictionary &	conn_spec,
		const std::vector< Dictionary > &	syn_specs
	)

Create connections.

References Dictionary::all_entries_accessed(), nest::ConnBuilder::connect(), nest::KernelManager::connection_manager, connruledict_, Dictionary::get(), Dictionary::init_access_flags(), nest::kernel(), Dictionary::known(), nest::KernelManager::node_manager, nest::names::rule(), set_connections_have_changed(), nest::Stopwatch< detailed_timer, threaded_timer >::start(), nest::Stopwatch< detailed_timer, threaded_timer >::stop(), sw_construction_connect, and nest::NodeManager::update_thread_local_node_data().

Referenced by nest::connect(), connect_arrays(), nest::ConnectionCreator::connect_to_target_(), nest::ConnectionCreator::connect_to_target_poisson_(), nest::ConnectionCreator::fixed_indegree_(), nest::ConnectionCreator::fixed_outdegree_(), and nest::BipartiteConnBuilder::single_connect_().

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◆ connect_()

void nest::ConnectionManager::connect_	(	Node &	source,
		Node &	target,
		const size_t	s_node_id,
		const size_t	tid,
		const synindex	syn_id,
		const Dictionary &	params,
		const double	delay = `numerics::nan`,
		const double	weight = `numerics::nan`
	)

private

connect_ is used to establish a connection between a sender and receiving node which both have proxies.

The parameters delay and weight have the default value numerics::nan. numerics::nan is a special value, which describes double values that are not a number. If delay or weight is omitted in an connect call, numerics::nan indicates this and weight/delay are set only, if they are valid.

Parameters

source	A reference to the sending Node.
target	A reference to the receiving Node.
s_node_id	The node ID of the sending Node.
tid	The thread of the target node.
syn_id	The synapse model to use.
params	The parameters for the connection.
delay	The delay of the connection (optional).
weight	The weight of the connection (optional).

References nest::ConnectorModel::add_connection(), nest::SourceTable::add_source(), check_primary_connections_, check_secondary_connections_, connections_, nest::ModelManager::get_connection_model(), has_primary_connections_, nest::ConnectorModel::has_property(), increase_connection_count(), nest::IS_PRIMARY, nest::kernel(), nest::KernelManager::model_manager, nest::REQUIRES_CLOPATH_ARCHIVING, nest::REQUIRES_EPROP_ARCHIVING, nest::REQUIRES_URBANCZIK_ARCHIVING, secondary_connections_exist_, nest::PerThreadBoolIndicator::set_true(), and source_table_.

Referenced by connect(), and connect().

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◆ connect_arrays()

void nest::ConnectionManager::connect_arrays	(	const long *	sources,
		const long *	targets,
		const double *	weights,
		const double *	delays,
		const std::vector< std::string > &	p_keys,
		const double *	p_values,
		size_t	n,
		const std::string &	syn_model
	)

References connect(), nest::KernelManager::connection_manager, Dictionary::find(), nest::ModelManager::get_connector_defaults(), nest::NodeManager::get_node_or_proxy(), nest::VPManager::get_num_threads(), nest::ModelManager::get_synapse_model_id(), nest::VPManager::get_thread_id(), nest::kernel(), nest::KernelManager::model_manager, nest::names::music_channel(), numerics::nan, nest::KernelManager::node_manager, nest::names::receptor_type(), set_connections_have_changed(), nest::Stopwatch< detailed_timer, threaded_timer >::start(), nest::Stopwatch< detailed_timer, threaded_timer >::stop(), sw_construction_connect, nest::names::synapse_label(), nest::NodeManager::update_thread_local_node_data(), and nest::KernelManager::vp_manager.

Referenced by nest::connect_arrays().

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◆ connect_from_device_()

void nest::ConnectionManager::connect_from_device_	(	Node &	source,
		Node &	target,
		const size_t	tid,
		const synindex	syn_id,
		const Dictionary &	params,
		const double	delay = `NAN`,
		const double	weight = `NAN`
	)

private

connect_from_device_ is used to establish a connection between a sender and receiving node if the sender does not have proxies.

The parameters delay and weight have the default value NAN. NAN is a special value in cmath, which describes double values that are not a number. If delay or weight is omitted in an connect call, NAN indicates this and weight/delay are set only, if they are valid.

Parameters

source	A reference to the sending Node.
target	A reference to the receiving Node.
s_node_id	The node ID of the sending Node.
tid	The thread of the target node.
syn_id	The synapse model to use.
params	The parameters for the connection.
delay	The delay of the connection (optional).
weight	The weight of the connection (optional).

References nest::TargetTableDevices::add_connection_from_device(), increase_connection_count(), and target_table_devices_.

Referenced by connect(), and connect().

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◆ connect_sonata()

void nest::ConnectionManager::connect_sonata	(	const Dictionary &	graph_specs,
		const long	hyberslab_size
	)

Connect nodes from SONATA specification.

This function instantiates the SonataConnector class and calls the class member function connect.

Parameters

graph_specs	Specification dictionary, see PyNEST `SonataNetwork._create_graph_specs` for details.
hyberslab_size	Size of the hyperslab to read in one read operation, applies to all HDF5 datasets.

References nest::KernelManager::connection_manager, nest::kernel(), nest::KernelManager::node_manager, set_connections_have_changed(), nest::Stopwatch< detailed_timer, threaded_timer >::start(), nest::Stopwatch< detailed_timer, threaded_timer >::stop(), sw_construction_connect, and nest::NodeManager::update_thread_local_node_data().

Referenced by nest::connect_sonata().

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◆ connect_to_device_()

void nest::ConnectionManager::connect_to_device_	(	Node &	source,
		Node &	target,
		const size_t	s_node_id,
		const size_t	tid,
		const synindex	syn_id,
		const Dictionary &	params,
		const double	delay = `NAN`,
		const double	weight = `NAN`
	)

private

connect_to_device_ is used to establish a connection between a sender and receiving node if the sender has proxies, and the receiver does not.

The parameters delay and weight have the default value NAN. NAN is a special value in cmath, which describes double values that are not a number. If delay or weight is omitted in an connect call, NAN indicates this and weight/delay are set only, if they are valid.

Parameters

source	A reference to the sending Node.
target	A reference to the receiving Node.
s_node_id	The node ID of the sending Node.
tid	The thread of the target node.
syn_id	The synapse model to use.
params	The parameters for the connection.
delay	The delay of the connection (optional).
weight	The weight of the connection (optional).

References nest::TargetTableDevices::add_connection_to_device(), increase_connection_count(), and target_table_devices_.

Referenced by connect(), and connect().

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◆ connect_tripartite()

void nest::ConnectionManager::connect_tripartite	(	NodeCollectionPTR	sources,
		NodeCollectionPTR	targets,
		NodeCollectionPTR	third,
		const Dictionary &	connectivity,
		const Dictionary &	third_connectivity,
		const std::map< std::string, std::vector< Dictionary > > &	synapse_specs
	)

Create tripartite connections.

Note: synapse_specs is dictionary {"primary": <syn_spec>, "third_in": <syn_spec>, "third_out": <syn_spec>}; all keys are optional

References Dictionary::all_entries_accessed(), nest::ConnBuilder::connect(), nest::KernelManager::connection_manager, Dictionary::get(), Dictionary::init_access_flags(), nest::kernel(), Dictionary::known(), nest::KernelManager::node_manager, nest::names::rule(), set_connections_have_changed(), nest::Stopwatch< detailed_timer, threaded_timer >::start(), nest::Stopwatch< detailed_timer, threaded_timer >::stop(), sw_construction_connect, and nest::NodeManager::update_thread_local_node_data().

Referenced by nest::connect_tripartite().

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◆ connection_required()

ConnectionManager::ConnectionType nest::ConnectionManager::connection_required	(	Node *&	source,
		Node *&	target,
		size_t	tid
	)

Check whether a connection between the given source and target nodes can be established on the given thread with id tid.

Returns: The type of connection as ConnectionType if the connection should be made, ConnectionType::NO_CONNECTION otherwise.

References CONNECT, CONNECT_FROM_DEVICE, CONNECT_TO_DEVICE, nest::NodeManager::get_node_or_proxy(), nest::VPManager::is_local_vp(), nest::kernel(), NO_CONNECTION, nest::VPManager::node_id_to_vp(), nest::KernelManager::node_manager, nest::KernelManager::vp_manager, and nest::VPManager::vp_to_thread().

Referenced by connect(), and connect().

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◆ connections_have_changed()

bool nest::ConnectionManager::connections_have_changed ( ) const

inline

Returns true if connection information needs to be communicated.

False otherwise.

References connections_have_changed_.

Referenced by get_connections().

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◆ delete_connections_()

void nest::ConnectionManager::delete_connections_ ( )

private

Deletes all connections.

References connections_.

Referenced by finalize().

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◆ deliver_secondary_events()

bool nest::ConnectionManager::deliver_secondary_events	(	const size_t	tid,
		const bool	called_from_wfr_update,
		std::vector< unsigned int > &	recv_buffer
	)

References connections_, nest::ModelManager::get_connection_model(), nest::ModelManager::get_connection_models(), nest::MPIManager::get_done_marker_position_in_secondary_events_recv_buffer(), nest::MPIManager::get_num_processes(), nest::ModelManager::get_secondary_event_prototype(), nest::SimulationManager::get_slice_origin(), nest::ConnectorModel::has_property(), nest::kernel(), nest::KernelManager::model_manager, nest::KernelManager::mpi_manager, secondary_recv_buffer_pos_, nest::KernelManager::simulation_manager, and nest::SUPPORTS_WFR.

Referenced by nest::EventDeliveryManager::deliver_secondary_events().

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◆ disconnect()

void nest::ConnectionManager::disconnect	(	const size_t	tid,
		const synindex	syn_id,
		const size_t	snode_id,
		const size_t	tnode_id
	)

References connections_, nest::SourceTable::disable_connection(), find_connection(), nest::invalid_synindex, num_connections_, and source_table_.

Referenced by nest::SPManager::delete_synapse(), and nest::SPManager::disconnect().

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◆ fill_target_buffer()

bool nest::ConnectionManager::fill_target_buffer	(	const size_t	tid,
		const size_t	rank_start,
		const size_t	rank_end,
		std::vector< TargetData > &	send_buffer_target_data,
		TargetSendBufferPosition &	send_buffer_position
	)

References nest::TargetSendBufferPosition::begin(), compressed_spike_data_, nest::SourceTable::compressed_spike_data_map_, nest::ModelManager::get_connection_model(), nest::SpikeData::get_lcid(), nest::MPIManager::get_process_id_of_node_id(), nest::MPIManager::get_recv_displacement_secondary_events_in_int(), get_secondary_recv_buffer_position(), nest::SpikeData::get_tid(), nest::ConnectorModel::has_property(), nest::TargetSendBufferPosition::idx(), nest::TargetSendBufferPosition::increase(), nest::TargetSendBufferPosition::is_chunk_filled(), nest::IS_PRIMARY, iteration_state_, nest::kernel(), nest::KernelManager::model_manager, nest::KernelManager::mpi_manager, nest::VPManager::node_id_to_lid(), nest::TargetData::reset_marker(), nest::TargetData::secondary_data, nest::TargetData::set_is_primary(), nest::TargetDataFields::set_lcid(), nest::SecondaryTargetDataFields::set_recv_buffer_pos(), nest::TargetData::set_source_lid(), nest::TargetData::set_source_tid(), nest::TargetDataFields::set_syn_id(), nest::SecondaryTargetDataFields::set_syn_id(), nest::TargetDataFields::set_tid(), source_table_, nest::TargetData::target_data, nest::KernelManager::vp_manager, and nest::VPManager::vp_to_thread().

Referenced by nest::EventDeliveryManager::collocate_target_data_buffers_compressed_().

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◆ finalize()

void nest::ConnectionManager::finalize ( const bool adjust_number_of_threads_or_rng_only )

overridevirtual

Take down manager after operation.

After this method has completed, all dynamic data structures created by the manager shall be deallocated and containers emptied. Plain variables need not be reset.

Note: Finalization of any given manager may depend on other managers not having been finalized yet. KernelManager::finalize() is responsible for calling the initialization routines on the specific managers in correct order, i.e., the opposite order of initialize() calls.

Parameters

adjust_number_of_threads_or_rng_only Pass true if calling from kernel_manager::change_number_of_threads() to limit operations to those necessary for thread adjustment.

See also: initialize()

Implements nest::ManagerInterface.

References Dictionary::clear(), compressed_spike_data_, connbuilder_factories_, connections_, connruledict_, delete_connections_(), nest::SourceTable::finalize(), nest::TargetTable::finalize(), nest::TargetTableDevices::finalize(), secondary_recv_buffer_pos_, source_table_, target_table_, target_table_devices_, thirdconnbuilder_factories_, and thirdconnruledict_.

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◆ find_connection()

size_t nest::ConnectionManager::find_connection	(	const size_t	tid,
		const synindex	syn_id,
		const size_t	snode_id,
		const size_t	tnode_id
	)

Find first non-disabled thread-local connection of given synapse type with given source and target node.

Returns: Local connection id (lcid) or invalid_index

References connections_, nest::SourceTable::find_first_source(), source_table_, and use_compressed_spikes_.

Referenced by disconnect().

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◆ get_compressed_spike_data()

const std::vector< SpikeData > & nest::ConnectionManager::get_compressed_spike_data	(	const synindex	syn_id,
		const size_t	idx
	)

inline

References compressed_spike_data_.

Referenced by nest::EventDeliveryManager::deliver_events_().

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◆ get_conn_builder()

BipartiteConnBuilder * nest::ConnectionManager::get_conn_builder	(	const std::string &	name,
		NodeCollectionPTR	sources,
		NodeCollectionPTR	targets,
		ThirdOutBuilder *	third_out,
		const Dictionary &	conn_spec,
		const std::vector< Dictionary > &	syn_specs
	)

Obtain builder for bipartite connections.

References connbuilder_factories_, connruledict_, Dictionary::get(), and Dictionary::known().

Referenced by nest::SPManager::disconnect().

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◆ get_connections() [1/2]

std::deque< ConnectionID > nest::ConnectionManager::get_connections ( const Dictionary & params )

Return connections between pairs of neurons.

The params dictionary can have the following entries: 'source' a token array with node IDs of source neurons. 'target' a token array with node IDs of target neuron. If either of these does not exist, all neuron are used for the respective entry. 'synapse_model' name of the synapse model, or all synapse models are searched. 'synapse_label' label (long) of the synapse, or all synapses are searched. The function then iterates all entries in source and collects the connection IDs to all neurons in target.

References nest::NodeManager::check_wfr_use(), connections_have_changed(), get_connections(), get_connections_has_been_called_, nest::ModelManager::get_num_connection_models(), nest::ModelManager::get_synapse_model_id(), nest::VPManager::get_thread_id(), nest::kernel(), nest::KernelManager::model_manager, nest::KernelManager::node_manager, nest::KernelManager::simulation_manager, nest::names::source(), nest::names::synapse_label(), nest::names::synapse_model(), nest::names::target(), nest::UNLABELED_CONNECTION, nest::SimulationManager::update_connection_infrastructure(), update_delay_extrema_(), and nest::KernelManager::vp_manager.

Referenced by nest::Layer< D >::dump_connections(), nest::get_connections(), and get_connections().

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◆ get_connections() [2/2]

void nest::ConnectionManager::get_connections	(	std::deque< ConnectionID > &	connectome,
		NodeCollectionPTR	source,
		NodeCollectionPTR	target,
		synindex	syn_id,
		long	synapse_label
	)		const

References nest::extend_connectome(), get_connections_(), get_connections_from_sources_(), get_connections_to_targets_(), get_num_connections(), nest::VPManager::get_thread_id(), is_source_table_cleared(), nest::kernel(), and nest::KernelManager::vp_manager.

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◆ get_connections_()

void nest::ConnectionManager::get_connections_	(	const size_t	tid,
		std::deque< ConnectionID > &	connectome,
		NodeCollectionPTR	source,
		NodeCollectionPTR	target,
		synindex	syn_id,
		long	synapse_label
	)		const

private

See get_connections()

References connections_, nest::ConnectorBase::get_connection(), nest::TargetTableDevices::get_connections(), nest::SourceTable::get_node_id(), nest::ConnectorBase::size(), source_table_, and target_table_devices_.

Referenced by get_connections().

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◆ get_connections_from_sources_()

void nest::ConnectionManager::get_connections_from_sources_	(	const size_t	tid,
		std::deque< ConnectionID > &	connectome,
		NodeCollectionPTR	source,
		NodeCollectionPTR	target,
		synindex	syn_id,
		long	synapse_label
	)		const

private

References connections_, nest::ConnectorBase::get_connection(), nest::ConnectorBase::get_connection_with_specified_targets(), nest::TargetTableDevices::get_connections(), nest::TargetTableDevices::get_connections_from_devices_(), nest::TargetTableDevices::get_connections_to_devices_(), nest::SourceTable::get_node_id(), nest::ConnectorBase::size(), source_table_, split_to_neuron_device_vectors_(), and target_table_devices_.

Referenced by get_connections().

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◆ get_connections_to_targets_()

void nest::ConnectionManager::get_connections_to_targets_	(	const size_t	tid,
		std::deque< ConnectionID > &	connectome,
		NodeCollectionPTR	source,
		NodeCollectionPTR	target,
		synindex	syn_id,
		long	synapse_label
	)		const

private

References connections_, nest::ConnectorBase::get_connection_with_specified_targets(), nest::TargetTableDevices::get_connections_from_devices_(), nest::TargetTableDevices::get_connections_to_devices_(), nest::SourceTable::get_node_id(), nest::ConnectorBase::size(), source_table_, split_to_neuron_device_vectors_(), and target_table_devices_.

Referenced by get_connections().

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◆ get_delay_checker()

DelayChecker & nest::ConnectionManager::get_delay_checker ( )

Returns the delay checker for the current thread.

References delay_checkers_, nest::VPManager::get_thread_id(), nest::kernel(), and nest::KernelManager::vp_manager.

Referenced by nest::GenericConnectorModel< ConnectionT >::add_connection(), nest::GenericConnectorModel< ConnectionT >::set_status(), nest::cont_delay_synapse< targetidentifierT >::set_status(), nest::Connection< targetidentifierT >::set_status(), and nest::GenericConnectorModel< ConnectionT >::used_default_delay().

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◆ get_device_connected()

bool nest::ConnectionManager::get_device_connected	(	size_t	tid,
		size_t	lcid
	)		const

inline

References nest::TargetTableDevices::is_device_connected(), and target_table_devices_.

Referenced by nest::StimulationBackendMPI::prepare().

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◆ get_keep_source_table()

bool nest::ConnectionManager::get_keep_source_table ( ) const

inline

Returns true if source table is kept after building network.

References keep_source_table_.

◆ get_max_delay()

long nest::ConnectionManager::get_max_delay ( ) const

inline

Return maximal connection delay, which is precomputed by update_delay_extrema_().

References max_delay_.

Referenced by nest::DelayChecker::assert_two_valid_delays_steps(), nest::DelayChecker::assert_valid_delay_ms(), nest::ClopathArchivingNode::init_clopath_buffers(), nest::EventDeliveryManager::init_moduli(), nest::RingBuffer::resize(), nest::MultRBuffer::resize(), nest::ListRingBuffer::resize(), nest::MultiChannelInputBuffer< num_channels >::resize(), nest::SliceRingBuffer::resize(), and nest::EventDeliveryManager::update_moduli().

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◆ get_max_delay_time_()

const Time nest::ConnectionManager::get_max_delay_time_ ( ) const

private

This method queries and finds the maximum delay of all local connections.

References delay_checkers_, and nest::Time::get_resolution().

Referenced by update_delay_extrema_().

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◆ get_min_delay()

long nest::ConnectionManager::get_min_delay ( ) const

inline

Return minimal connection delay, which is precomputed by update_delay_extrema_().

References min_delay_.

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◆ get_min_delay_time_()

const Time nest::ConnectionManager::get_min_delay_time_ ( ) const

private

This method queries and finds the minimum delay of all local connections.

References delay_checkers_, and nest::Time::pos_inf().

Referenced by update_delay_extrema_().

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◆ get_next_target_data()

bool nest::ConnectionManager::get_next_target_data	(	const size_t	tid,
		const size_t	rank_start,
		const size_t	rank_end,
		size_t &	target_rank,
		TargetData &	next_target_data
	)

inline

References nest::SourceTable::get_next_target_data(), and source_table_.

Referenced by nest::EventDeliveryManager::collocate_target_data_buffers_().

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◆ get_num_connections() [1/2]

size_t nest::ConnectionManager::get_num_connections ( ) const

Returns the number of connections in the network.

References num_connections_.

Referenced by get_connections(), nest::ModelManager::get_connector_defaults(), get_status(), nest::EpropSynapseCommonProperties::set_status(), and nest::EpropSynapseBSSHSLM2020CommonProperties::set_status().

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◆ get_num_connections() [2/2]

size_t nest::ConnectionManager::get_num_connections ( const synindex syn_id ) const

Returns the number of connections of this synapse type.

References num_connections_.

◆ get_num_connections_()

size_t nest::ConnectionManager::get_num_connections_	(	const size_t	tid,
		const synindex	syn_id
	)		const

inlineprivate

References connections_.

Referenced by compute_compressed_secondary_recv_buffer_positions().

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◆ get_num_target_data()

size_t nest::ConnectionManager::get_num_target_data ( const size_t tid ) const

private

References connections_, nest::SourceTable::num_unique_sources(), and source_table_.

Referenced by compute_target_data_buffer_size().

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◆ get_remote_targets_of_local_node()

const std::vector< Target > & nest::ConnectionManager::get_remote_targets_of_local_node	(	const size_t	tid,
		const size_t	lid
	)		const

inline

References nest::TargetTable::get_targets(), and target_table_.

Referenced by nest::EventDeliveryManager::send_off_grid_remote(), and nest::EventDeliveryManager::send_remote().

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◆ get_secondary_recv_buffer_position()

size_t nest::ConnectionManager::get_secondary_recv_buffer_position	(	const size_t	tid,
		const synindex	syn_id,
		const size_t	lcid
	)		const

inline

Returns read position in MPI receive buffer for secondary connections.

References secondary_recv_buffer_pos_.

Referenced by fill_target_buffer(), and nest::SourceTable::populate_target_data_fields_().

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◆ get_secondary_send_buffer_positions()

const std::vector< size_t > & nest::ConnectionManager::get_secondary_send_buffer_positions	(	const size_t	tid,
		const size_t	lid,
		const synindex	syn_id
	)		const

inline

References nest::TargetTable::get_secondary_send_buffer_positions(), and target_table_.

Referenced by nest::EventDeliveryManager::send_secondary().

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◆ get_source_node_id()

size_t nest::ConnectionManager::get_source_node_id	(	const size_t	tid,
		const synindex	syn_id,
		const size_t	lcid
	)

inline

References nest::SourceTable::get_node_id(), and source_table_.

Referenced by nest::Event::retrieve_sender_node_id_from_source_table().

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◆ get_source_node_ids_()

void nest::ConnectionManager::get_source_node_ids_	(	const size_t	tid,
		const synindex	syn_id,
		const size_t	tnode_id,
		std::vector< size_t > &	sources
	)

private

References connections_, nest::SourceTable::get_source_node_ids(), and source_table_.

Referenced by get_sources().

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◆ get_sources()

void nest::ConnectionManager::get_sources	(	const std::vector< size_t > &	targets,
		const size_t	syn_id,
		std::vector< std::vector< size_t > > &	sources
	)

References nest::VPManager::get_num_threads(), get_source_node_ids_(), nest::kernel(), and nest::KernelManager::vp_manager.

Referenced by nest::SPManager::delete_synapses_from_post().

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◆ get_status()

void nest::ConnectionManager::get_status ( Dictionary & )

overridevirtual

Retrieve the status of the manager.

Note: This would ideally be a const function. However, some managers delay the update of internal variables up to the point where they are needed (e.g., before reporting their values to the user, or before simulate is called). An example for this pattern is the call to update_delay_extrema_() right at the beginning of ConnectionManager::get_status().

See also: set_status()

Implements nest::ManagerInterface.

References nest::names::connection_rules(), connruledict_, nest::Time::get_ms(), get_num_connections(), nest::Stopwatch< detailed_timer, threaded_timer >::get_status(), nest::names::keep_source_table(), keep_source_table_, nest::names::max_delay(), max_delay_, nest::names::min_delay(), min_delay_, nest::names::num_connections(), sw_construction_connect, nest::names::time_construction_connect(), nest::names::time_construction_connect_cpu(), update_delay_extrema_(), nest::names::use_compressed_spikes(), and use_compressed_spikes_.

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◆ get_stdp_eps()

double nest::ConnectionManager::get_stdp_eps ( ) const

inline

References stdp_eps_.

Referenced by nest::ArchivingNode::get_history().

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◆ get_synapse_status()

Dictionary nest::ConnectionManager::get_synapse_status	(	const size_t	source_node_id,
		const size_t	target_node_id,
		const size_t	tid,
		const synindex	syn_id,
		const size_t	lcid
	)		const

References nest::ModelManager::assert_valid_syn_id(), connections_, nest::ModelManager::get_connection_model(), nest::ConnectorModel::get_name(), nest::NodeManager::get_node_or_proxy(), nest::TargetTableDevices::get_synapse_status_from_device(), nest::TargetTableDevices::get_synapse_status_to_device(), nest::kernel(), nest::KernelManager::model_manager, nest::KernelManager::node_manager, nest::names::port(), nest::names::source(), nest::names::synapse_id(), nest::names::synapse_model(), target_table_devices_, and nest::names::target_thread().

Referenced by nest::Layer< D >::dump_connections(), nest::get_connection_status(), and nest::get_connection_status().

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◆ get_target_node_id()

size_t nest::ConnectionManager::get_target_node_id	(	const size_t	tid,
		const synindex	syn_id,
		const size_t	lcid
	)		const

inline

References connections_.

◆ get_targets()

void nest::ConnectionManager::get_targets	(	const std::vector< size_t > &	sources,
		const size_t	syn_id,
		const std::string &	post_synaptic_element,
		std::vector< std::vector< size_t > > &	targets
	)

References connections_, nest::SourceTable::find_first_source(), nest::VPManager::get_num_threads(), nest::kernel(), source_table_, and nest::KernelManager::vp_manager.

Referenced by nest::SPManager::delete_synapses_from_pre().

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◆ get_third_conn_builder()

ThirdOutBuilder * nest::ConnectionManager::get_third_conn_builder	(	const std::string &	name,
		NodeCollectionPTR	sources,
		NodeCollectionPTR	targets,
		ThirdInBuilder *	third_in,
		const Dictionary &	conn_spec,
		const std::vector< Dictionary > &	syn_specs
	)

Obtain builder for bipartite connections.

References Dictionary::get(), Dictionary::known(), thirdconnbuilder_factories_, and thirdconnruledict_.

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◆ get_user_set_delay_extrema()

bool nest::ConnectionManager::get_user_set_delay_extrema ( ) const

References delay_checkers_.

Referenced by nest::KernelManager::change_number_of_threads(), and update_delay_extrema_().

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◆ has_primary_connections()

bool nest::ConnectionManager::has_primary_connections ( ) const

inline

References has_primary_connections_.

◆ increase_connection_count()

void nest::ConnectionManager::increase_connection_count	(	const size_t	tid,
		const synindex	syn_id
	)

private

Increases the connection count.

References nest::MAX_LCID, and num_connections_.

Referenced by connect_(), connect_from_device_(), and connect_to_device_().

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◆ initialize()

void nest::ConnectionManager::initialize ( const bool adjust_number_of_threads_or_rng_only )

overridevirtual

Prepare manager for operation.

After this method has completed, the manager should be completely initialized and "ready for action".

Note: Initialization of any given manager may depend on other managers having been initialized before. KernelManager::initialize() is responsible for calling the initialization routines on the specific managers in correct order.

Parameters

adjust_number_of_threads_or_rng_only Pass true if calling from kernel_manager::change_number_of_threads() or RandomManager::get_status() to limit operations to those necessary for thread adjustment or switch or re-seeding of RNG.

See also: finalize()

Implements nest::ManagerInterface.

References check_primary_connections_, check_secondary_connections_, compressed_spike_data_, connections_, connections_have_changed_, delay_checkers_, get_connections_has_been_called_, nest::ModelManager::get_num_connection_models(), nest::VPManager::get_num_threads(), nest::VPManager::get_thread_id(), has_primary_connections_, nest::SourceTable::initialize(), nest::TargetTable::initialize(), nest::TargetTableDevices::initialize(), nest::PerThreadBoolIndicator::initialize(), keep_source_table_, nest::kernel(), max_delay_, min_delay_, nest::KernelManager::model_manager, num_connections_, nest::Stopwatch< detailed_timer, threaded_timer >::reset(), secondary_connections_exist_, secondary_recv_buffer_pos_, source_table_, stdp_eps_, sw_construction_connect, target_table_, target_table_devices_, use_compressed_spikes_, and nest::KernelManager::vp_manager.

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◆ initialize_iteration_state()

void nest::ConnectionManager::initialize_iteration_state ( )

Set iteration_state_ entries for all threads to beginning of compressed_spike_data_map_.

References nest::SourceTable::compressed_spike_data_map_, nest::VPManager::get_num_threads(), iteration_state_, nest::kernel(), source_table_, and nest::KernelManager::vp_manager.

Referenced by nest::SimulationManager::update_connection_infrastructure().

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◆ is_source_table_cleared()

bool nest::ConnectionManager::is_source_table_cleared ( ) const

inline

Returns true if source table was cleared.

References nest::SourceTable::is_cleared(), and source_table_.

Referenced by get_connections().

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◆ no_targets_to_process()

void nest::ConnectionManager::no_targets_to_process ( const size_t tid )

inline

References nest::SourceTable::no_targets_to_process(), and source_table_.

Referenced by nest::EventDeliveryManager::collocate_target_data_buffers_().

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◆ prepare_target_table()

void nest::ConnectionManager::prepare_target_table ( const size_t tid )

inline

References nest::TargetTable::prepare(), and target_table_.

Referenced by nest::EventDeliveryManager::gather_target_data(), and nest::EventDeliveryManager::gather_target_data_compressed().

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◆ register_conn_builder()

template<typename ConnBuilder >

void nest::ConnectionManager::register_conn_builder ( const std::string & name )

Add a connectivity rule, i.e.

the respective ConnBuilderFactory.

References connbuilder_factories_, connruledict_, and Dictionary::known().

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◆ register_third_conn_builder()

template<typename ThirdConnBuilder >

void nest::ConnectionManager::register_third_conn_builder ( const std::string & name )

Add a connectivity rule, i.e.

the respective ConnBuilderFactory.

References Dictionary::known(), thirdconnbuilder_factories_, and thirdconnruledict_.

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◆ reject_last_target_data()

void nest::ConnectionManager::reject_last_target_data ( const size_t tid )

inline

References nest::SourceTable::reject_last_target_data(), and source_table_.

Referenced by nest::EventDeliveryManager::collocate_target_data_buffers_().

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◆ remove_disabled_connections_()

void nest::ConnectionManager::remove_disabled_connections_ ( const size_t tid )

private

Removes disabled connections (of structural plasticity)

References connections_, nest::SourceTable::remove_disabled_sources(), source_table_, and use_compressed_spikes_.

Referenced by sort_connections().

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◆ reset_source_table_entry_point()

void nest::ConnectionManager::reset_source_table_entry_point ( const size_t tid )

inline

References nest::SourceTable::reset_entry_point(), and source_table_.

Referenced by nest::EventDeliveryManager::gather_target_data().

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◆ resize_connections()

void nest::ConnectionManager::resize_connections ( )

References nest::VPManager::assert_thread_parallel(), connections_, nest::kernel(), nest::SourceTable::resize_sources(), nest::TargetTableDevices::resize_to_number_of_synapse_types(), source_table_, target_table_devices_, and nest::KernelManager::vp_manager.

Referenced by nest::ModelManager::copy_connection_model_(), and nest::ModelManager::register_specific_connection_model_().

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◆ resize_target_table_devices_to_number_of_neurons()

void nest::ConnectionManager::resize_target_table_devices_to_number_of_neurons ( )

inline

References nest::TargetTableDevices::resize_to_number_of_neurons(), and target_table_devices_.

Referenced by nest::NodeManager::add_node().

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◆ resize_target_table_devices_to_number_of_synapse_types()

void nest::ConnectionManager::resize_target_table_devices_to_number_of_synapse_types ( )

inline

References nest::TargetTableDevices::resize_to_number_of_synapse_types(), and target_table_devices_.

Referenced by nest::NodeManager::add_node().

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◆ restore_source_table_entry_point()

void nest::ConnectionManager::restore_source_table_entry_point ( const size_t tid )

inline

References nest::SourceTable::restore_entry_point(), and source_table_.

Referenced by nest::EventDeliveryManager::gather_target_data().

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◆ restructure_connection_tables()

void nest::ConnectionManager::restructure_connection_tables ( const size_t tid )

inline

Deletes TargetTable and resets processed flags of SourceTable.

This function must be called if connections are created after connections have been communicated previously. It basically restores the connection infrastructure to a state where all information only exists on the postsynaptic side.

References nest::TargetTable::clear(), nest::SourceTable::is_cleared(), nest::SourceTable::reset_processed_flags(), source_table_, and target_table_.

Referenced by nest::SimulationManager::update_connection_infrastructure().

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◆ save_source_table_entry_point()

void nest::ConnectionManager::save_source_table_entry_point ( const size_t tid )

inline

References nest::SourceTable::save_entry_point(), and source_table_.

Referenced by nest::EventDeliveryManager::collocate_target_data_buffers_(), and nest::EventDeliveryManager::gather_target_data().

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◆ secondary_connections_exist()

bool nest::ConnectionManager::secondary_connections_exist ( ) const

inline

References secondary_connections_exist_.

◆ send()

void nest::ConnectionManager::send	(	const size_t	tid,
		const synindex	syn_id,
		const size_t	lcid,
		const std::vector< ConnectorModel * > &	cm,
		Event &	e
	)

inline

References connections_.

Referenced by nest::EventDeliveryManager::deliver_events_().

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◆ send_from_device()

void nest::ConnectionManager::send_from_device	(	const size_t	tid,
		const size_t	ldid,
		Event &	e
	)

inline

Send event e to all targets of source device ldid (local device id)

References nest::kernel(), nest::TargetTableDevices::send_from_device(), and target_table_devices_.

Referenced by nest::EventDeliveryManager::send_local_(), and nest::EventDeliveryManager::send_local_().

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◆ send_local()

void nest::ConnectionManager::send_local	(	size_t	t,
		Node &	source,
		Event &	e
	)

Send event e to all targets of node source on thread t.

◆ send_to_devices() [1/2]

void nest::ConnectionManager::send_to_devices	(	const size_t	tid,
		const size_t	source_node_id,
		Event &	e
	)

inline

Send event e to all device targets of source source_node_id.

References nest::kernel(), nest::TargetTableDevices::send_to_device(), and target_table_devices_.

Referenced by nest::EventDeliveryManager::send(), and nest::EventDeliveryManager::send_secondary().

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◆ send_to_devices() [2/2]

void nest::ConnectionManager::send_to_devices	(	const size_t	tid,
		const size_t	source_node_id,
		SecondaryEvent &	e
	)

inline

References nest::kernel(), nest::TargetTableDevices::send_to_device(), and target_table_devices_.

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◆ set_connections_have_changed()

void nest::ConnectionManager::set_connections_have_changed ( )

Sets flag indicating whether connection information needs to be communicated to true.

References connections_have_changed_, get_connections_has_been_called_, nest::kernel(), LOG, and nest::WARNING.

Referenced by connect(), connect_arrays(), nest::connect_layers(), connect_sonata(), connect_tripartite(), nest::SPManager::disconnect(), and nest::SPManager::update_structural_plasticity().

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◆ set_source_has_more_targets()

void nest::ConnectionManager::set_source_has_more_targets	(	const size_t	tid,
		const synindex	syn_id,
		const size_t	lcid,
		const bool	more_targets
	)

inline

References connections_.

Referenced by nest::SourceTable::collect_compressible_sources(), and nest::SourceTable::get_next_target_data().

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◆ set_status()

void nest::ConnectionManager::set_status ( const Dictionary & )

overridevirtual

Set the status of the manager.

See also: get_status()

Implements nest::ManagerInterface.

References delay_checkers_, nest::names::keep_source_table(), keep_source_table_, nest::kernel(), nest::names::max_delay(), nest::names::min_delay(), update_delay_extrema_(), nest::names::use_compressed_spikes(), and use_compressed_spikes_.

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◆ set_stdp_eps()

void nest::ConnectionManager::set_stdp_eps ( const double stdp_eps )

References nest::Time::get_resolution(), nest::INFO, LOG, and stdp_eps_.

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◆ set_synapse_status()

void nest::ConnectionManager::set_synapse_status	(	const size_t	source_node_id,
		const size_t	target_node_id,
		const size_t	tid,
		const synindex	syn_id,
		const size_t	lcid,
		const Dictionary &	dict
	)

References nest::ModelManager::assert_valid_syn_id(), connections_, nest::ModelManager::get_connection_model(), nest::NodeManager::get_node_or_proxy(), nest::kernel(), nest::KernelManager::model_manager, nest::KernelManager::node_manager, nest::TargetTableDevices::set_synapse_status_from_device(), nest::TargetTableDevices::set_synapse_status_to_device(), and target_table_devices_.

Referenced by nest::set_connection_status(), and nest::set_connection_status().

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◆ sort_connections()

void nest::ConnectionManager::sort_connections ( const size_t tid )

Sorts connections in the presynaptic infrastructure by increasing source node ID.

References connections_, nest::SourceTable::get_thread_local_sources(), nest::SourceTable::is_cleared(), remove_disabled_connections_(), source_table_, and use_compressed_spikes_.

Referenced by nest::SimulationManager::update_connection_infrastructure().

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◆ split_to_neuron_device_vectors_()

void nest::ConnectionManager::split_to_neuron_device_vectors_	(	const size_t	tid,
		NodeCollectionPTR	nodecollection,
		std::vector< size_t > &	neuron_node_ids,
		std::vector< size_t > &	device_node_ids
	)		const

private

Splits a TokenArray of node IDs to two vectors containing node IDs of neurons and node IDs of devices.

References nest::NodeManager::get_node_or_proxy(), nest::kernel(), and nest::KernelManager::node_manager.

Referenced by get_connections_from_sources_(), and get_connections_to_targets_().

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◆ sync_has_primary_connections()

void nest::ConnectionManager::sync_has_primary_connections ( )

References nest::MPIManager::any_true(), has_primary_connections_, nest::kernel(), and nest::KernelManager::mpi_manager.

Referenced by nest::SimulationManager::update_connection_infrastructure().

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◆ trigger_update_weight()

void nest::ConnectionManager::trigger_update_weight	(	const long	vt_node_id,
		const std::vector< spikecounter > &	dopa_spikes,
		const double	t_trig
	)

Triggered by volume transmitter in update.

Triggeres updates for all connectors of dopamine synapses that are registered with the volume transmitter with node_id vt_node_id.

References connections_, nest::VPManager::get_thread_id(), nest::kernel(), and nest::KernelManager::vp_manager.

Referenced by nest::volume_transmitter::update().

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◆ unset_connections_have_changed()

void nest::ConnectionManager::unset_connections_have_changed ( )

Sets flag indicating whether connection information needs to be communicated to false.

References connections_have_changed_.

Referenced by nest::SimulationManager::update_connection_infrastructure().

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◆ update_delay_extrema_()

void nest::ConnectionManager::update_delay_extrema_ ( )

private

Update delay extrema to current values.

Note: This entails MPI communication.

References nest::MPIManager::communicate(), get_max_delay_time_(), get_min_delay_time_(), nest::MPIManager::get_rank(), nest::Time::get_resolution(), nest::Time::get_steps(), get_user_set_delay_extrema(), nest::kernel(), max_delay_, min_delay_, nest::KernelManager::mpi_manager, and nest::Time::pos_inf().

Referenced by get_connections(), get_status(), nest::SimulationManager::prepare(), and set_status().

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◆ use_compressed_spikes()

bool nest::ConnectionManager::use_compressed_spikes ( ) const

inline

Returns whether spikes should be compressed.

Implies that connections will be sorted by source.

References use_compressed_spikes_.

Referenced by nest::EventDeliveryManager::deliver_events_().

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◆ valid_connection_rule()

bool nest::ConnectionManager::valid_connection_rule ( std::string rule_name )

inline

References connruledict_, and Dictionary::known().

Referenced by nest::SPManager::disconnect().

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Friends And Related Symbol Documentation

◆ SimulationManager

friend class SimulationManager

friend

Member Data Documentation

◆ buffer_pos_of_source_node_id_syn_id_

std::map< size_t, size_t > nest::ConnectionManager::buffer_pos_of_source_node_id_syn_id_

private

Referenced by compute_compressed_secondary_recv_buffer_positions().

◆ check_primary_connections_

PerThreadBoolIndicator nest::ConnectionManager::check_primary_connections_

private

Check for primary connections (spikes) on each thread.

Referenced by connect_(), and initialize().

◆ check_secondary_connections_

PerThreadBoolIndicator nest::ConnectionManager::check_secondary_connections_

private

Check for secondary connections (e.g., gap junctions) on each thread.

Referenced by connect_(), and initialize().

◆ compressed_spike_data_

std::vector< std::vector< std::vector< SpikeData > > > nest::ConnectionManager::compressed_spike_data_

private

A structure to hold "unpacked" spikes on the postsynaptic side if spike compression is enabled.

Internally arranged in a 3d structure: synapses|sources|target_threads

Referenced by collect_compressed_spike_data(), fill_target_buffer(), finalize(), get_compressed_spike_data(), and initialize().

◆ connbuilder_factories_

std::vector< GenericBipartiteConnBuilderFactory* > nest::ConnectionManager::connbuilder_factories_

private

ConnBuilder factories, indexed by connruledict_ elements.

Referenced by finalize(), get_conn_builder(), and register_conn_builder().

◆ connections_

std::vector< std::vector< ConnectorBase* > > nest::ConnectionManager::connections_

private

A structure to hold the Connector objects which in turn hold the connection information.

Corresponds to a three dimensional structure: threads|synapses|connections

Referenced by compute_compressed_secondary_recv_buffer_positions(), connect_(), delete_connections_(), deliver_secondary_events(), disconnect(), finalize(), find_connection(), get_connections_(), get_connections_from_sources_(), get_connections_to_targets_(), get_num_connections_(), get_num_target_data(), get_source_node_ids_(), get_synapse_status(), get_target_node_id(), get_targets(), initialize(), remove_disabled_connections_(), resize_connections(), send(), set_source_has_more_targets(), set_synapse_status(), sort_connections(), and trigger_update_weight().

◆ connections_have_changed_

bool nest::ConnectionManager::connections_have_changed_

private

True if new connections have been created since startup or last call to simulate.

Referenced by connections_have_changed(), initialize(), set_connections_have_changed(), and unset_connections_have_changed().

◆ connruledict_

Dictionary nest::ConnectionManager::connruledict_

private

Dictionary for connection rules.

Referenced by connect(), finalize(), get_conn_builder(), get_status(), register_conn_builder(), and valid_connection_rule().

◆ delay_checkers_

std::vector< DelayChecker > nest::ConnectionManager::delay_checkers_

private

Referenced by calibrate(), get_delay_checker(), get_max_delay_time_(), get_min_delay_time_(), get_user_set_delay_extrema(), initialize(), and set_status().

◆ get_connections_has_been_called_

bool nest::ConnectionManager::get_connections_has_been_called_

private

true if GetConnections has been called.

Referenced by get_connections(), initialize(), and set_connections_have_changed().

◆ has_primary_connections_

bool nest::ConnectionManager::has_primary_connections_

private

Whether primary connections (spikes) exist.

Referenced by connect_(), has_primary_connections(), initialize(), and sync_has_primary_connections().

◆ iteration_state_

std::vector< std::pair< size_t, std::map< size_t, CSDMapEntry >::const_iterator > > nest::ConnectionManager::iteration_state_

private

For each thread, store (syn_id, compressed_spike_data_map_::iterator) pair for next iteration while filling target buffers.

Referenced by fill_target_buffer(), and initialize_iteration_state().

◆ keep_source_table_

bool nest::ConnectionManager::keep_source_table_

private

Whether to keep source table after connection setup is complete.

Referenced by clean_source_table(), clear_source_table(), get_keep_source_table(), get_status(), initialize(), and set_status().

◆ max_delay_

long nest::ConnectionManager::max_delay_

private

Value of the largest delay in the network in steps.

Referenced by get_max_delay(), get_status(), initialize(), and update_delay_extrema_().

◆ min_delay_

long nest::ConnectionManager::min_delay_

private

Value of the smallest delay in the network.

Referenced by get_min_delay(), get_status(), initialize(), and update_delay_extrema_().

◆ num_connections_

std::vector< std::vector< size_t > > nest::ConnectionManager::num_connections_

private

A structure to count the number of synapses of a specific type.

Arranged in a 2d structure: threads|synapsetypes.

Referenced by disconnect(), get_num_connections(), get_num_connections(), increase_connection_count(), and initialize().

◆ secondary_connections_exist_

bool nest::ConnectionManager::secondary_connections_exist_

private

Whether secondary connections (e.g., gap junctions) exist.

Referenced by check_secondary_connections_exist(), connect_(), initialize(), and secondary_connections_exist().

◆ secondary_recv_buffer_pos_

std::vector< std::vector< std::vector< size_t > > > nest::ConnectionManager::secondary_recv_buffer_pos_

private

Stores absolute position in receive buffer of secondary events.

structure: threads|synapses|position

Referenced by compute_compressed_secondary_recv_buffer_positions(), deliver_secondary_events(), finalize(), get_secondary_recv_buffer_position(), and initialize().

◆ source_table_

SourceTable nest::ConnectionManager::source_table_

private

A structure to hold the node IDs of presynaptic neurons during postsynaptic connection creation, before the connection information has been transferred to the presynaptic side.

Internally arranged in a 3d structure: threads|synapses|node IDs

Referenced by clean_source_table(), clear_compressed_spike_data_map(), clear_source_table(), collect_compressed_spike_data(), compute_compressed_secondary_recv_buffer_positions(), connect_(), disconnect(), fill_target_buffer(), finalize(), find_connection(), get_connections_(), get_connections_from_sources_(), get_connections_to_targets_(), get_next_target_data(), get_num_target_data(), get_source_node_id(), get_source_node_ids_(), get_targets(), initialize(), initialize_iteration_state(), is_source_table_cleared(), no_targets_to_process(), reject_last_target_data(), remove_disabled_connections_(), reset_source_table_entry_point(), resize_connections(), restore_source_table_entry_point(), restructure_connection_tables(), save_source_table_entry_point(), and sort_connections().

◆ stdp_eps_

double nest::ConnectionManager::stdp_eps_

private

Maximum distance between (double) spike times in STDP that is still considered 0.

See issue #894

Referenced by get_stdp_eps(), initialize(), and set_stdp_eps().

◆ sw_construction_connect

Stopwatch< StopwatchGranularity::Normal, StopwatchParallelism::MasterOnly > nest::ConnectionManager::sw_construction_connect

Referenced by connect(), connect_arrays(), nest::connect_layers(), connect_sonata(), connect_tripartite(), get_status(), and initialize().

◆ target_table_

TargetTable nest::ConnectionManager::target_table_

private

A structure to hold the information about targets for each neuron on the presynaptic side.

Internally arranged in a 3d structure: threads|localnodes|targets

Referenced by add_target(), compress_secondary_send_buffer_pos(), finalize(), get_remote_targets_of_local_node(), get_secondary_send_buffer_positions(), initialize(), prepare_target_table(), and restructure_connection_tables().

◆ target_table_devices_

TargetTableDevices nest::ConnectionManager::target_table_devices_

private

Referenced by connect_from_device_(), connect_to_device_(), finalize(), get_connections_(), get_connections_from_sources_(), get_connections_to_targets_(), get_device_connected(), get_synapse_status(), initialize(), resize_connections(), resize_target_table_devices_to_number_of_neurons(), resize_target_table_devices_to_number_of_synapse_types(), send_from_device(), send_to_devices(), send_to_devices(), and set_synapse_status().

◆ thirdconnbuilder_factories_

std::vector< GenericThirdConnBuilderFactory* > nest::ConnectionManager::thirdconnbuilder_factories_

private

Third-factor ConnBuilder factories, indexed by thirdconnruledict_ elements.

Referenced by finalize(), get_third_conn_builder(), and register_third_conn_builder().

◆ thirdconnruledict_

Dictionary nest::ConnectionManager::thirdconnruledict_

private

Dictionary for third-factor connection rules.

Referenced by finalize(), get_third_conn_builder(), and register_third_conn_builder().

◆ use_compressed_spikes_

bool nest::ConnectionManager::use_compressed_spikes_

private

Whether to use spike compression; if a neuron has targets on multiple threads of a process, this switch makes sure that only a single packet is sent to the process instead of one packet per target thread; implies sort_connections_by_source_ = true; for more details see the discussion and sketch in https://github.com/nest/nest-simulator/pull/1338.

Referenced by collect_compressed_spike_data(), find_connection(), get_status(), initialize(), remove_disabled_connections_(), set_status(), sort_connections(), and use_compressed_spikes().

The documentation for this class was generated from the following files:

	NEST main@caf0ae8

Public Types

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Friends

Member Enumeration Documentation

◆ ConnectionType

Constructor & Destructor Documentation

◆ ConnectionManager()

◆ ~ConnectionManager()

Member Function Documentation

◆ add_target()

◆ calibrate()

◆ check_secondary_connections_exist()

◆ clean_source_table()

◆ clear_compressed_spike_data_map()

◆ clear_source_table()

◆ collect_compressed_spike_data()

◆ compress_secondary_send_buffer_pos()

◆ compute_compressed_secondary_recv_buffer_positions()

◆ compute_target_data_buffer_size()

◆ connect() [1/3]

◆ connect() [2/3]

◆ connect() [3/3]

◆ connect_()

◆ connect_arrays()

◆ connect_from_device_()

◆ connect_sonata()

◆ connect_to_device_()

◆ connect_tripartite()

◆ connection_required()

◆ connections_have_changed()

◆ delete_connections_()

◆ deliver_secondary_events()

◆ disconnect()

◆ fill_target_buffer()

◆ finalize()

◆ find_connection()

◆ get_compressed_spike_data()

◆ get_conn_builder()

◆ get_connections() [1/2]

◆ get_connections() [2/2]

◆ get_connections_()

◆ get_connections_from_sources_()

◆ get_connections_to_targets_()

◆ get_delay_checker()

◆ get_device_connected()

◆ get_keep_source_table()

◆ get_max_delay()

◆ get_max_delay_time_()

◆ get_min_delay()

◆ get_min_delay_time_()

◆ get_next_target_data()

◆ get_num_connections() [1/2]

◆ get_num_connections() [2/2]

◆ get_num_connections_()

◆ get_num_target_data()

◆ get_remote_targets_of_local_node()

◆ get_secondary_recv_buffer_position()

◆ get_secondary_send_buffer_positions()

◆ get_source_node_id()

◆ get_source_node_ids_()

◆ get_sources()

◆ get_status()

◆ get_stdp_eps()

◆ get_synapse_status()

◆ get_target_node_id()

◆ get_targets()

◆ get_third_conn_builder()

◆ get_user_set_delay_extrema()

◆ has_primary_connections()

◆ increase_connection_count()

◆ initialize()

◆ initialize_iteration_state()

◆ is_source_table_cleared()

◆ no_targets_to_process()

◆ prepare_target_table()

◆ register_conn_builder()

◆ register_third_conn_builder()