void
nest::SPBuilder::sp_connect( GIDCollection sources, GIDCollection targets )
{
connect_( sources, targets );
// check if any exceptions have been raised
for ( size_t thr = 0; thr < kernel().vp_manager.get_num_threads(); ++thr )
if ( exceptions_raised_.at( thr ).valid() )
throw WrappedThreadException( *( exceptions_raised_.at( thr ) ) );
}
/**
* Now we can delete synapses with or without structural plasticity
*/
void
nest::ConnBuilder::disconnect()
{
if ( pre_synaptic_element_name != "" && post_synaptic_element_name != "" )
{
sp_disconnect_();
}
else
{
disconnect_();
}
// check if any exceptions have been raised
for ( index thr = 0; thr < kernel().vp_manager.get_num_threads(); ++thr )
if ( exceptions_raised_.at( thr ).valid() )
throw WrappedThreadException( *( exceptions_raised_.at( thr ) ) );
}
/**
* Now we can connect with or without structural plasticity
*/
void
nest::ConnBuilder::connect()
{
if ( symmetric_ && not supports_symmetric() )
throw NotImplemented(
"This connection rule does not support symmetric connections." );
if ( pre_synaptic_element_name != "" && post_synaptic_element_name != "" )
{
if ( symmetric_ )
throw NotImplemented(
"Symmetric connections are not supported in combination with "
"structural plasticity." );
sp_connect_();
}
else
{
connect_();
if ( symmetric_ )
{
// call reset on all parameters
if ( weight_ )
weight_->reset();
if ( delay_ )
delay_->reset();
for ( ConnParameterMap::const_iterator it = synapse_params_.begin();
it != synapse_params_.end();
++it )
{
it->second->reset();
}
std::swap( sources_, targets_ );
connect_();
std::swap( sources_, targets_ ); // re-establish original state
}
}
// check if any exceptions have been raised
for ( size_t thr = 0; thr < kernel().vp_manager.get_num_threads(); ++thr )
if ( exceptions_raised_.at( thr ).valid() )
throw WrappedThreadException( *( exceptions_raised_.at( thr ) ) );
}
void
NodeManager::prepare_nodes()
{
assert( kernel().is_initialized() );
/* We initialize the buffers of each node and calibrate it. */
size_t num_active_nodes = 0; // counts nodes that will be updated
size_t num_active_wfr_nodes = 0; // counts nodes that use waveform relaxation
std::vector< lockPTR< WrappedThreadException > > exceptions_raised(
kernel().vp_manager.get_num_threads() );
#ifdef _OPENMP
#pragma omp parallel reduction( + : num_active_nodes, num_active_wfr_nodes )
{
size_t t = kernel().vp_manager.get_thread_id();
#else
for ( index t = 0; t < kernel().vp_manager.get_num_threads(); ++t )
{
#endif
// We prepare nodes in a parallel region. Therefore, we need to catch
// exceptions here and then handle them after the parallel region.
try
{
for ( std::vector< Node* >::iterator it = nodes_vec_[ t ].begin();
it != nodes_vec_[ t ].end();
++it )
{
prepare_node_( *it );
if ( not( *it )->is_frozen() )
{
++num_active_nodes;
if ( ( *it )->node_uses_wfr() )
{
++num_active_wfr_nodes;
}
}
}
}
catch ( std::exception& e )
{
// so throw the exception after parallel region
exceptions_raised.at( t ) =
lockPTR< WrappedThreadException >( new WrappedThreadException( e ) );
}
} // end of parallel section / end of for threads
// check if any exceptions have been raised
for ( index thr = 0; thr < kernel().vp_manager.get_num_threads(); ++thr )
{
if ( exceptions_raised.at( thr ).valid() )
{
throw WrappedThreadException( *( exceptions_raised.at( thr ) ) );
}
}
std::ostringstream os;
std::string tmp_str = num_active_nodes == 1 ? " node" : " nodes";
os << "Preparing " << num_active_nodes << tmp_str << " for simulation.";
if ( num_active_wfr_nodes != 0 )
{
tmp_str = num_active_wfr_nodes == 1 ? " uses " : " use ";
os << " " << num_active_wfr_nodes << " of them" << tmp_str
<< "iterative solution techniques.";
}
num_active_nodes_ = num_active_nodes;
LOG( M_INFO, "NodeManager::prepare_nodes", os.str() );
}
void
NodeManager::post_run_cleanup()
{
#ifdef _OPENMP
#pragma omp parallel
{
index t = kernel().vp_manager.get_thread_id();
#else // clang-format off
for ( index t = 0; t < kernel().vp_manager.get_num_threads(); ++t )
{
#endif // clang-format on
for ( size_t idx = 0; idx < local_nodes_.size(); ++idx )
{
Node* node = local_nodes_.get_node_by_index( idx );
if ( node != 0 )
{
if ( node->num_thread_siblings() > 0 )
{
node->get_thread_sibling( t )->post_run_cleanup();
}
else
{
if ( static_cast< index >( node->get_thread() ) == t )
{
node->post_run_cleanup();
}
}
}
}
}
}
void
nest::SimulationManager::update_()
{
// to store done values of the different threads
std::vector< bool > done;
bool done_all = true;
delay old_to_step;
std::vector< lockPTR< WrappedThreadException > > exceptions_raised(
kernel().vp_manager.get_num_threads() );
// parallel section begins
#pragma omp parallel
{
const int thrd = kernel().vp_manager.get_thread_id();
do
{
if ( print_time_ )
gettimeofday( &t_slice_begin_, NULL );
if ( kernel().sp_manager.is_structural_plasticity_enabled()
&& ( clock_.get_steps() + from_step_ )
% kernel().sp_manager.get_structural_plasticity_update_interval()
== 0 )
{
for ( std::vector< Node* >::const_iterator i =
kernel().node_manager.get_nodes_on_thread( thrd ).begin();
i != kernel().node_manager.get_nodes_on_thread( thrd ).end();
++i )
{
( *i )->update_synaptic_elements(
Time( Time::step( clock_.get_steps() + from_step_ ) ).get_ms() );
}
#pragma omp barrier
#pragma omp single
{
kernel().sp_manager.update_structural_plasticity();
}
// Remove 10% of the vacant elements
for ( std::vector< Node* >::const_iterator i =
kernel().node_manager.get_nodes_on_thread( thrd ).begin();
i != kernel().node_manager.get_nodes_on_thread( thrd ).end();
++i )
{
( *i )->decay_synaptic_elements_vacant();
}
}
if ( from_step_ == 0 ) // deliver only at beginning of slice
{
kernel().event_delivery_manager.deliver_events( thrd );
#ifdef HAVE_MUSIC
// advance the time of music by one step (min_delay * h) must
// be done after deliver_events_() since it calls
// music_event_out_proxy::handle(), which hands the spikes over to
// MUSIC *before* MUSIC time is advanced
// wait until all threads are done -> synchronize
#pragma omp barrier
// the following block is executed by the master thread only
// the other threads are enforced to wait at the end of the block
#pragma omp master
{
// advance the time of music by one step (min_delay * h) must
// be done after deliver_events_() since it calls
// music_event_out_proxy::handle(), which hands the spikes over to
// MUSIC *before* MUSIC time is advanced
if ( slice_ > 0 )
kernel().music_manager.advance_music_time();
// the following could be made thread-safe
kernel().music_manager.update_music_event_handlers(
clock_, from_step_, to_step_ );
}
// end of master section, all threads have to synchronize at this point
#pragma omp barrier
#endif
}
// preliminary update of nodes that use waveform relaxtion
if ( kernel().node_manager.any_node_uses_wfr() )
{
#pragma omp single
{
// if the end of the simulation is in the middle
// of a min_delay_ step, we need to make a complete
// step in the wfr_update and only do
// the partial step in the final update
// needs to be done in omp single since to_step_ is a scheduler
// variable
old_to_step = to_step_;
if ( to_step_ < kernel().connection_manager.get_min_delay() )
to_step_ = kernel().connection_manager.get_min_delay();
}
bool max_iterations_reached = true;
const std::vector< Node* >& thread_local_wfr_nodes =
kernel().node_manager.get_wfr_nodes_on_thread( thrd );
for ( long_t n = 0; n < wfr_max_iterations_; ++n )
{
bool done_p = true;
// this loop may be empty for those threads
// that do not have any nodes requiring wfr_update
for ( std::vector< Node* >::const_iterator i =
thread_local_wfr_nodes.begin();
i != thread_local_wfr_nodes.end();
++i )
done_p = wfr_update_( *i ) && done_p;
// add done value of thread p to done vector
#pragma omp critical
done.push_back( done_p );
// parallel section ends, wait until all threads are done -> synchronize
#pragma omp barrier
// the following block is executed by a single thread
// the other threads wait at the end of the block
#pragma omp single
{
// set done_all
for ( size_t i = 0; i < done.size(); i++ )
done_all = done[ i ] && done_all;
// gather SecondaryEvents (e.g. GapJunctionEvents)
kernel().event_delivery_manager.gather_events( done_all );
// reset done and done_all
//(needs to be in the single threaded part)
done_all = true;
done.clear();
}
// deliver SecondaryEvents generated during wfr_update
// returns the done value over all threads
done_p = kernel().event_delivery_manager.deliver_events( thrd );
if ( done_p )
{
max_iterations_reached = false;
break;
}
} // of for (wfr_max_iterations) ...
#pragma omp single
{
to_step_ = old_to_step;
if ( max_iterations_reached )
{
std::string msg = String::compose(
"Maximum number of iterations reached at interval %1-%2 ms",
clock_.get_ms(),
clock_.get_ms() + to_step_ * Time::get_resolution().get_ms() );
LOG( M_WARNING, "SimulationManager::wfr_update", msg );
}
}
} // of if(any_node_uses_wfr)
// end of preliminary update
const std::vector< Node* >& thread_local_nodes =
kernel().node_manager.get_nodes_on_thread( thrd );
for (
std::vector< Node* >::const_iterator node = thread_local_nodes.begin();
node != thread_local_nodes.end();
++node )
{
// We update in a parallel region. Therefore, we need to catch
// exceptions here and then handle them after the parallel region.
try
{
if ( not( *node )->is_frozen() )
( *node )->update( clock_, from_step_, to_step_ );
}
catch ( std::exception& e )
{
// so throw the exception after parallel region
exceptions_raised.at( thrd ) = lockPTR< WrappedThreadException >(
new WrappedThreadException( e ) );
terminate_ = true;
}
}
// parallel section ends, wait until all threads are done -> synchronize
#pragma omp barrier
// the following block is executed by the master thread only
// the other threads are enforced to wait at the end of the block
#pragma omp master
{
// gather only at end of slice
if ( to_step_ == kernel().connection_manager.get_min_delay() )
kernel().event_delivery_manager.gather_events( true );
advance_time_();
if ( SLIsignalflag != 0 )
{
LOG( M_INFO,
"SimulationManager::update",
"Simulation exiting on user signal." );
terminate_ = true;
}
if ( print_time_ )
{
gettimeofday( &t_slice_end_, NULL );
print_progress_();
}
}
// end of master section, all threads have to synchronize at this point
#pragma omp barrier
} while ( ( to_do_ != 0 ) && ( !terminate_ ) );
// End of the slice, we update the number of synaptic element
for ( std::vector< Node* >::const_iterator i =
kernel().node_manager.get_nodes_on_thread( thrd ).begin();
i != kernel().node_manager.get_nodes_on_thread( thrd ).end();
++i )
{
( *i )->update_synaptic_elements(
Time( Time::step( clock_.get_steps() + to_step_ ) ).get_ms() );
}
} // end of #pragma parallel omp
// check if any exceptions have been raised
for ( index thrd = 0; thrd < kernel().vp_manager.get_num_threads(); ++thrd )
if ( exceptions_raised.at( thrd ).valid() )
throw WrappedThreadException( *( exceptions_raised.at( thrd ) ) );
}