void
nest::SimulationManager::cleanup()
{
if ( not prepared_ )
{
std::string msg = "Cleanup called without calling Prepare.";
LOG( M_ERROR, "SimulationManager::cleanup", msg );
throw KernelException();
}
if ( not simulated_ )
{
return;
}
// Check for synchronicity of global rngs over processes
if ( kernel().mpi_manager.get_num_processes() > 1 )
{
if ( not kernel().mpi_manager.grng_synchrony(
kernel().rng_manager.get_grng()->ulrand( 100000 ) ) )
{
throw KernelException(
"In SimulationManager::cleanup(): "
"Global Random Number Generators are not "
"in sync at end of simulation." );
}
}
kernel().node_manager.finalize_nodes();
prepared_ = false;
}
void
nest::RNGManager::create_grng_()
{
// create new grng
LOG( M_INFO, "Network::create_grng_", "Creating new default global RNG" );
// create default RNG with default seed
#ifdef HAVE_GSL
grng_ = librandom::RngPtr( new librandom::GslRandomGen(
gsl_rng_knuthran2002, librandom::RandomGen::DefaultSeed ) );
#else
grng_ = librandom::RandomGen::create_knuthlfg_rng(
librandom::RandomGen::DefaultSeed );
#endif
if ( !grng_ )
{
LOG( M_ERROR, "Network::create_grng_", "Error initializing knuthlfg" );
throw KernelException();
}
/*
The seed for the global rng should be different from the seeds
of the local rngs_ for each thread seeded with 1,..., n_vps.
*/
long s = 0;
grng_seed_ = s;
grng_->seed( s );
}
synindex
ConnectionManager::copy_synapse_prototype( synindex old_id, std::string new_name )
{
// we can assert here, as nestmodule checks this for us
assert( !synapsedict_->known( new_name ) );
int new_id = prototypes_[ 0 ].size();
if ( new_id == invalid_synindex ) // we wrapped around (=255), maximal id of synapse_model = 254
{
net_.message( SLIInterpreter::M_ERROR,
"ConnectionManager::copy_synapse_prototype",
"CopyModel cannot generate another synapse. Maximal synapse model count of 255 exceeded." );
throw KernelException( "Synapse model count exceeded" );
}
assert( new_id != invalid_synindex );
// if the copied synapse is a secondary connector model the synid of the copy has to
// be mapped to the corresponding secondary event type
if ( not get_synapse_prototype( old_id ).is_primary() )
{
( get_synapse_prototype( old_id ).get_event() )->add_syn_id( new_id );
}
for ( thread t = 0; t < net_.get_num_threads(); ++t )
{
prototypes_[ t ].push_back( get_synapse_prototype( old_id ).clone( new_name ) );
prototypes_[ t ][ new_id ]->set_syn_id( new_id );
}
synapsedict_->insert( new_name, new_id );
return new_id;
}
index
ModelManager::copy_synapse_model_( index old_id, Name new_name )
{
size_t new_id = prototypes_[ 0 ].size();
if ( new_id == invalid_synindex ) // we wrapped around (=255), maximal id of
// synapse_model = 254
{
LOG( M_ERROR,
"ModelManager::copy_synapse_model_",
"CopyModel cannot generate another synapse. Maximal synapse model count "
"of 255 exceeded." );
throw KernelException( "Synapse model count exceeded" );
}
assert( new_id != invalid_synindex );
// if the copied synapse is a secondary connector model the synid of the copy
// has to be mapped to the corresponding secondary event type
if ( not get_synapse_prototype( old_id ).is_primary() )
{
( get_synapse_prototype( old_id ).get_event() )->add_syn_id( new_id );
}
for ( thread t = 0;
t < static_cast< thread >( kernel().vp_manager.get_num_threads() );
++t )
{
prototypes_[ t ].push_back(
get_synapse_prototype( old_id ).clone( new_name.toString() ) );
prototypes_[ t ][ new_id ]->set_syn_id( new_id );
}
synapsedict_->insert( new_name, new_id );
return new_id;
}
void
nest::RNGManager::create_rngs_()
{
// if old generators exist, remove them; since rng_ contains
// lockPTRs, we don't have to worry about deletion
if ( !rng_.empty() )
{
LOG( M_INFO,
"Network::create_rngs_",
"Deleting existing random number generators" );
rng_.clear();
}
LOG( M_INFO, "Network::create_rngs_", "Creating default RNGs" );
rng_seeds_.resize( kernel().vp_manager.get_num_virtual_processes() );
for ( index i = 0; i < static_cast< index >(
kernel().vp_manager.get_num_virtual_processes() );
++i )
{
unsigned long s = i + 1;
if ( kernel().vp_manager.is_local_vp( i ) )
{
/*
We have to ensure that each thread is provided with a different
stream of random numbers. The seeding method for Knuth's LFG
generator guarantees that different seeds yield non-overlapping
random number sequences.
We therefore have to seed with known numbers: using random
seeds here would run the risk of using the same seed twice.
For simplicity, we use 1 .. n_vps.
*/
#ifdef HAVE_GSL
librandom::RngPtr rng(
new librandom::GslRandomGen( gsl_rng_knuthran2002, s ) );
#else
librandom::RngPtr rng = librandom::RandomGen::create_knuthlfg_rng( s );
#endif
if ( !rng )
{
LOG( M_ERROR, "Network::create_rngs_", "Error initializing knuthlfg" );
throw KernelException();
}
rng_.push_back( rng );
}
rng_seeds_[ i ] = s;
}
}
void
nest::SimulationManager::assert_valid_simtime( Time const& t )
{
if ( t == Time::ms( 0.0 ) )
{
return;
}
if ( t < Time::step( 1 ) )
{
LOG( M_ERROR,
"SimulationManager::run",
String::compose( "Simulation time must be >= %1 ms (one time step).",
Time::get_resolution().get_ms() ) );
throw KernelException();
}
if ( t.is_finite() )
{
Time time1 = clock_ + t;
if ( not time1.is_finite() )
{
std::string msg = String::compose(
"A clock overflow will occur after %1 of %2 ms. Please reset network "
"clock first!",
( Time::max() - clock_ ).get_ms(),
t.get_ms() );
LOG( M_ERROR, "SimulationManager::run", msg );
throw KernelException();
}
}
else
{
std::string msg = String::compose(
"The requested simulation time exceeds the largest time NEST can handle "
"(T_max = %1 ms). Please use a shorter time!",
Time::max().get_ms() );
LOG( M_ERROR, "SimulationManager::run", msg );
throw KernelException();
}
}
void Model::set_threads_(thread t)
{
for (size_t i = 0; i < memory_.size(); ++i)
if ( memory_[i].get_instantiations() > 0 )
throw KernelException();
std::vector<sli::pool> tmp(t);
memory_.swap(tmp);
for (size_t i = 0; i < memory_.size(); ++i)
init_memory_(memory_[i]);
}
nest::index
nest::SourceTable::get_gid( const thread tid,
const synindex syn_id,
const index lcid ) const
{
if ( not kernel().connection_manager.get_keep_source_table() )
{
throw KernelException(
"Cannot use SourceTable::get_gid when get_keep_source_table is false" );
}
return sources_[ tid ][ syn_id ][ lcid ].get_gid();
}
size_t
nest::SimulationManager::prepare_simulation_()
{
assert( to_do_ != 0 ); // This is checked in simulate()
// find shortest and longest delay across all MPI processes
// this call sets the member variables
kernel().connection_manager.update_delay_extrema_();
kernel().event_delivery_manager.init_moduli();
// Check for synchronicity of global rngs over processes.
// We need to do this ahead of any simulation in case random numbers
// have been consumed on the SLI level.
if ( kernel().mpi_manager.get_num_processes() > 1 )
{
if ( !kernel().mpi_manager.grng_synchrony(
kernel().rng_manager.get_grng()->ulrand( 100000 ) ) )
{
LOG( M_ERROR,
"SimulationManager::simulate",
"Global Random Number Generators are not synchronized prior to "
"simulation." );
throw KernelException();
}
}
// if at the beginning of a simulation, set up spike buffers
if ( !simulated_ )
kernel().event_delivery_manager.configure_spike_buffers();
kernel().node_manager.ensure_valid_thread_local_ids();
const size_t num_active_nodes = kernel().node_manager.prepare_nodes();
kernel().model_manager.create_secondary_events_prototypes();
// we have to do enter_runtime after prepre_nodes, since we use
// calibrate to map the ports of MUSIC devices, which has to be done
// before enter_runtime
if ( !simulated_ ) // only enter the runtime mode once
{
double tick = Time::get_resolution().get_ms()
* kernel().connection_manager.get_min_delay();
kernel().music_manager.enter_runtime( tick );
}
return num_active_nodes;
}
void
nest::SimulationManager::finalize_simulation_()
{
if ( not simulated_ )
return;
// Check for synchronicity of global rngs over processes
// TODO: This seems double up, there is such a test at end of simulate()
if ( kernel().mpi_manager.get_num_processes() > 1 )
if ( !kernel().mpi_manager.grng_synchrony( kernel().rng_manager.get_grng()->ulrand( 100000 ) ) )
{
LOG( M_ERROR,
"SimulationManager::simulate",
"Global Random Number Generators are not synchronized after simulation." );
throw KernelException();
}
kernel().node_manager.finalize_nodes();
}
index NodeManager::add_node( index mod, long n ) // no_p
{
assert( current_ != 0 );
assert( root_ != 0 );
if ( mod >= kernel().model_manager.get_num_node_models() )
{
throw UnknownModelID( mod );
}
if ( n < 1 )
{
throw BadProperty();
}
const thread n_threads = kernel().vp_manager.get_num_threads();
assert( n_threads > 0 );
const index min_gid = local_nodes_.get_max_gid() + 1;
const index max_gid = min_gid + n;
Model* model = kernel().model_manager.get_model( mod );
assert( model != 0 );
model->deprecation_warning( "Create" );
/* current_ points to the instance of the current subnet on thread 0.
The following code makes subnet a pointer to the wrapper container
containing the instances of the current subnet on all threads.
*/
const index subnet_gid = current_->get_gid();
Node* subnet_node = local_nodes_.get_node_by_gid( subnet_gid );
assert( subnet_node != 0 );
SiblingContainer* subnet_container =
dynamic_cast< SiblingContainer* >( subnet_node );
assert( subnet_container != 0 );
assert( subnet_container->num_thread_siblings()
== static_cast< size_t >( n_threads ) );
assert( subnet_container->get_thread_sibling( 0 ) == current_ );
if ( max_gid > local_nodes_.max_size() || max_gid < min_gid )
{
LOG( M_ERROR,
"NodeManager::add:node",
"Requested number of nodes will overflow the memory." );
LOG( M_ERROR, "NodeManager::add:node", "No nodes were created." );
throw KernelException( "OutOfMemory" );
}
kernel().modelrange_manager.add_range( mod, min_gid, max_gid - 1 );
if ( model->potential_global_receiver()
and kernel().mpi_manager.get_num_rec_processes() > 0 )
{
// In this branch we create nodes for global receivers
const int n_per_process = n / kernel().mpi_manager.get_num_rec_processes();
const int n_per_thread = n_per_process / n_threads + 1;
// We only need to reserve memory on the ranks on which we
// actually create nodes. In this if-branch ---> Only on recording
// processes
if ( kernel().mpi_manager.get_rank()
>= kernel().mpi_manager.get_num_sim_processes() )
{
local_nodes_.reserve( std::ceil( static_cast< double >( max_gid )
/ kernel().mpi_manager.get_num_sim_processes() ) );
for ( thread t = 0; t < n_threads; ++t )
{
// Model::reserve() reserves memory for n ADDITIONAL nodes on thread t
model->reserve_additional( t, n_per_thread );
}
}
for ( size_t gid = min_gid; gid < max_gid; ++gid )
{
const thread vp = kernel().vp_manager.suggest_rec_vp( get_n_gsd() );
const thread t = kernel().vp_manager.vp_to_thread( vp );
if ( kernel().vp_manager.is_local_vp( vp ) )
{
Node* newnode = model->allocate( t );
newnode->set_gid_( gid );
newnode->set_model_id( mod );
newnode->set_thread( t );
newnode->set_vp( vp );
newnode->set_has_proxies( true );
newnode->set_local_receiver( false );
local_nodes_.add_local_node( *newnode ); // put into local nodes list
current_->add_node( newnode ); // and into current subnet, thread 0.
}
else
{
local_nodes_.add_remote_node( gid ); // ensures max_gid is correct
current_->add_remote_node( gid, mod );
}
increment_n_gsd();
}
}
else if ( model->has_proxies() )
{
// In this branch we create nodes for all GIDs which are on a local thread
const int n_per_process = n / kernel().mpi_manager.get_num_sim_processes();
const int n_per_thread = n_per_process / n_threads + 1;
// We only need to reserve memory on the ranks on which we
// actually create nodes. In this if-branch ---> Only on
// simulation processes
if ( kernel().mpi_manager.get_rank()
< kernel().mpi_manager.get_num_sim_processes() )
{
// TODO: This will work reasonably for round-robin. The extra 50 entries
// are for subnets and devices.
local_nodes_.reserve(
std::ceil( static_cast< double >( max_gid )
/ kernel().mpi_manager.get_num_sim_processes() ) + 50 );
for ( thread t = 0; t < n_threads; ++t )
{
// Model::reserve() reserves memory for n ADDITIONAL nodes on thread t
// reserves at least one entry on each thread, nobody knows why
model->reserve_additional( t, n_per_thread );
}
}
size_t gid;
if ( kernel().vp_manager.is_local_vp(
kernel().vp_manager.suggest_vp( min_gid ) ) )
{
gid = min_gid;
}
else
{
gid = next_local_gid_( min_gid );
}
size_t next_lid = current_->global_size() + gid - min_gid;
// The next loop will not visit every node, if more than one rank is
// present.
// Since we already know what range of gids will be created, we can tell the
// current subnet the range and subsequent calls to
// `current_->add_remote_node()`
// become irrelevant.
current_->add_gid_range( min_gid, max_gid - 1 );
// min_gid is first valid gid i should create, hence ask for the first local
// gid after min_gid-1
while ( gid < max_gid )
{
const thread vp = kernel().vp_manager.suggest_vp( gid );
const thread t = kernel().vp_manager.vp_to_thread( vp );
if ( kernel().vp_manager.is_local_vp( vp ) )
{
Node* newnode = model->allocate( t );
newnode->set_gid_( gid );
newnode->set_model_id( mod );
newnode->set_thread( t );
newnode->set_vp( vp );
local_nodes_.add_local_node( *newnode ); // put into local nodes list
current_->add_node( newnode ); // and into current subnet, thread 0.
// lid setting is wrong, if a range is set, as the subnet already
// assumes,
// the nodes are available.
newnode->set_lid_( next_lid );
const size_t next_gid = next_local_gid_( gid );
next_lid += next_gid - gid;
gid = next_gid;
}
else
{
++gid; // brutal fix, next_lid has been set in if-branch
}
}
// if last gid is not on this process, we need to add it as a remote node
if ( not kernel().vp_manager.is_local_vp(
kernel().vp_manager.suggest_vp( max_gid - 1 ) ) )
{
local_nodes_.add_remote_node( max_gid - 1 ); // ensures max_gid is correct
current_->add_remote_node( max_gid - 1, mod );
}
}
else if ( not model->one_node_per_process() )
{
// We allocate space for n containers which will hold the threads
// sorted. We use SiblingContainers to store the instances for
// each thread to exploit the very efficient memory allocation for
// nodes.
//
// These containers are registered in the global nodes_ array to
// provide access to the instances both for manipulation by SLI
// functions and so that NodeManager::calibrate() can discover the
// instances and register them for updating.
//
// The instances are also registered with the instance of the
// current subnet for the thread to which the created instance
// belongs. This is mainly important so that the subnet structure
// is preserved on all VPs. Node enumeration is done on by the
// registration with the per-thread instances.
//
// The wrapper container can be addressed under the GID assigned
// to no-proxy node created. If this no-proxy node is NOT a
// container (e.g. a device), then each instance can be retrieved
// by giving the respective thread-id to get_node(). Instances of
// SiblingContainers cannot be addressed individually.
//
// The allocation of the wrapper containers is spread over threads
// to balance memory load.
size_t container_per_thread = n / n_threads + 1;
// since we create the n nodes on each thread, we reserve the full load.
for ( thread t = 0; t < n_threads; ++t )
{
model->reserve_additional( t, n );
siblingcontainer_model_->reserve_additional( t, container_per_thread );
static_cast< Subnet* >( subnet_container->get_thread_sibling( t ) )
->reserve( n );
}
// The following loop creates n nodes. For each node, a wrapper is created
// and filled with one instance per thread, in total n * n_thread nodes in
// n wrappers.
local_nodes_.reserve(
std::ceil( static_cast< double >( max_gid )
/ kernel().mpi_manager.get_num_sim_processes() ) + 50 );
for ( index gid = min_gid; gid < max_gid; ++gid )
{
thread thread_id = kernel().vp_manager.vp_to_thread(
kernel().vp_manager.suggest_vp( gid ) );
// Create wrapper and register with nodes_ array.
SiblingContainer* container = static_cast< SiblingContainer* >(
siblingcontainer_model_->allocate( thread_id ) );
container->set_model_id(
-1 ); // mark as pseudo-container wrapping replicas, see reset_network()
container->reserve( n_threads ); // space for one instance per thread
container->set_gid_( gid );
local_nodes_.add_local_node( *container );
// Generate one instance of desired model per thread
for ( thread t = 0; t < n_threads; ++t )
{
Node* newnode = model->allocate( t );
newnode->set_gid_( gid ); // all instances get the same global id.
newnode->set_model_id( mod );
newnode->set_thread( t );
newnode->set_vp( kernel().vp_manager.thread_to_vp( t ) );
// Register instance with wrapper
// container has one entry for each thread
container->push_back( newnode );
// Register instance with per-thread instance of enclosing subnet.
static_cast< Subnet* >( subnet_container->get_thread_sibling( t ) )
->add_node( newnode );
}
}
}
else
{
// no proxies and one node per process
// this is used by MUSIC proxies
// Per r9700, this case is only relevant for music_*_proxy models,
// which have a single instance per MPI process.
for ( index gid = min_gid; gid < max_gid; ++gid )
{
Node* newnode = model->allocate( 0 );
newnode->set_gid_( gid );
newnode->set_model_id( mod );
newnode->set_thread( 0 );
newnode->set_vp( kernel().vp_manager.thread_to_vp( 0 ) );
// Register instance
local_nodes_.add_local_node( *newnode );
// and into current subnet, thread 0.
current_->add_node( newnode );
}
}
// set off-grid spike communication if necessary
if ( model->is_off_grid() )
{
kernel().event_delivery_manager.set_off_grid_communication( true );
LOG( M_INFO,
"NodeManager::add_node",
"Neuron models emitting precisely timed spikes exist: "
"the kernel property off_grid_spiking has been set to true.\n\n"
"NOTE: Mixing precise-spiking and normal neuron models may "
"lead to inconsistent results." );
}
return max_gid - 1;
}
void
nest::SimulationManager::set_status( const DictionaryDatum& d )
{
// Create an instance of time converter here to capture the current
// representation of time objects: TICS_PER_MS and TICS_PER_STEP
// will be stored in time_converter.
// This object can then be used to convert times in steps
// (e.g. Connection::delay_) or tics to the new representation.
// We pass this object to ConnectionManager::calibrate to update
// all time objects in the connection system to the new representation.
// MH 08-04-14
TimeConverter time_converter;
double_t time;
if ( updateValue< double_t >( d, "time", time ) )
{
if ( time != 0.0 )
throw BadProperty( "The simulation time can only be set to 0.0." );
if ( clock_ > TimeZero )
{
// reset only if time has passed
LOG( M_WARNING,
"SimulationManager::set_status",
"Simulation time reset to t=0.0. Resetting the simulation time is not "
"fully supported in NEST at present. Some spikes may be lost, and "
"stimulating devices may behave unexpectedly. PLEASE REVIEW YOUR "
"SIMULATION OUTPUT CAREFULLY!" );
clock_ = Time::step( 0 );
from_step_ = 0;
slice_ = 0;
// clear all old spikes
kernel().event_delivery_manager.configure_spike_buffers();
}
}
updateValue< bool >( d, "print_time", print_time_ );
// tics_per_ms and resolution must come after local_num_thread /
// total_num_threads because they might reset the network and the time
// representation
nest::double_t tics_per_ms = 0.0;
bool tics_per_ms_updated =
updateValue< nest::double_t >( d, "tics_per_ms", tics_per_ms );
double_t resd = 0.0;
bool res_updated = updateValue< double_t >( d, "resolution", resd );
if ( tics_per_ms_updated || res_updated )
{
if ( kernel().node_manager.size() > 1 ) // root always exists
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Cannot change time representation after nodes have been created. "
"Please call ResetKernel first." );
throw KernelException();
}
else if ( has_been_simulated() ) // someone may have simulated empty network
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Cannot change time representation after the network has been "
"simulated. Please call ResetKernel first." );
throw KernelException();
}
else if ( kernel().connection_manager.get_num_connections() != 0 )
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Cannot change time representation after connections have been "
"created. Please call ResetKernel first." );
throw KernelException();
}
else if ( res_updated && tics_per_ms_updated ) // only allow TICS_PER_MS to
// be changed together with
// resolution
{
if ( resd < 1.0 / tics_per_ms )
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Resolution must be greater than or equal to one tic. Value "
"unchanged." );
throw KernelException();
}
else
{
nest::Time::set_resolution( tics_per_ms, resd );
// adjust to new resolution
clock_.calibrate();
// adjust delays in the connection system to new resolution
kernel().connection_manager.calibrate( time_converter );
kernel().model_manager.calibrate( time_converter );
LOG( M_INFO,
"SimulationManager::set_status",
"tics per ms and resolution changed." );
// make sure that wfr communication interval is always greater or equal
// to resolution if no wfr is used explicitly set wfr_comm_interval
// to resolution because communication in every step is needed
if ( wfr_comm_interval_ < Time::get_resolution().get_ms()
|| not use_wfr_ )
{
wfr_comm_interval_ = Time::get_resolution().get_ms();
}
}
}
else if ( res_updated ) // only resolution changed
{
if ( resd < Time::get_ms_per_tic() )
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Resolution must be greater than or equal to one tic. Value "
"unchanged." );
throw KernelException();
}
else
{
Time::set_resolution( resd );
clock_.calibrate(); // adjust to new resolution
// adjust delays in the connection system to new resolution
kernel().connection_manager.calibrate( time_converter );
kernel().model_manager.calibrate( time_converter );
LOG( M_INFO,
"SimulationManager::set_status",
"Temporal resolution changed." );
// make sure that wfr communication interval is always greater or equal
// to resolution if no wfr is used explicitly set wfr_comm_interval
// to resolution because communication in every step is needed
if ( wfr_comm_interval_ < Time::get_resolution().get_ms()
|| not use_wfr_ )
{
wfr_comm_interval_ = Time::get_resolution().get_ms();
}
}
}
else
{
LOG( M_ERROR,
"SimulationManager::set_status",
"change of tics_per_step requires simultaneous specification of "
"resolution." );
throw KernelException();
}
}
// The decision whether the waveform relaxation is used
// must be set before nodes are created.
// Important: wfr_comm_interval_ may change depending on use_wfr_
bool wfr;
if ( updateValue< bool >( d, "use_wfr", wfr ) )
{
if ( kernel().node_manager.size() > 1 )
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Cannot enable/disable usage of waveform relaxation after nodes have "
"been created. Please call ResetKernel first." );
throw KernelException();
}
else
{
use_wfr_ = wfr;
// if no wfr is used explicitly set wfr_comm_interval to resolution
// because communication in every step is needed
if ( not use_wfr_ )
{
wfr_comm_interval_ = Time::get_resolution().get_ms();
}
}
}
// wfr_comm_interval_ can only be changed if use_wfr_ is true and before
// connections are created. If use_wfr_ is false wfr_comm_interval_ is set to
// the resolution whenever the resolution changes.
double_t wfr_interval;
if ( updateValue< double_t >( d, "wfr_comm_interval", wfr_interval ) )
{
if ( not use_wfr_ )
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Cannot set waveform communication interval when usage of waveform "
"relaxation is disabled. Set use_wfr to true first." );
throw KernelException();
}
else if ( kernel().connection_manager.get_num_connections() != 0 )
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Cannot change waveform communication interval after connections have "
"been created. Please call ResetKernel first." );
throw KernelException();
}
else if ( wfr_interval < Time::get_resolution().get_ms() )
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Communication interval of the waveform relaxation must be greater or "
"equal to the resolution of the simulation." );
throw KernelException();
}
else
{
LOG( M_INFO,
"SimulationManager::set_status",
"Waveform communication interval changed successfully. " );
wfr_comm_interval_ = wfr_interval;
}
}
// set the convergence tolerance for the waveform relaxation method
double_t tol;
if ( updateValue< double_t >( d, "wfr_tol", tol ) )
{
if ( tol < 0.0 )
LOG( M_ERROR,
"SimulationManager::set_status",
"Tolerance must be zero or positive" );
else
wfr_tol_ = tol;
}
// set the maximal number of iterations for the waveform relaxation method
long max_iter;
if ( updateValue< long >( d, "wfr_max_iterations", max_iter ) )
{
if ( max_iter <= 0 )
LOG( M_ERROR,
"SimulationManager::set_status",
"Maximal number of iterations for the waveform relaxation must be "
"positive. To disable waveform relaxation set use_wfr instead." );
else
wfr_max_iterations_ = max_iter;
}
// set the interpolation order for the waveform relaxation method
long interp_order;
if ( updateValue< long >( d, "wfr_interpolation_order", interp_order ) )
{
if ( ( interp_order < 0 ) || ( interp_order == 2 ) || ( interp_order > 3 ) )
LOG( M_ERROR,
"SimulationManager::set_status",
"Interpolation order must be 0, 1, or 3." );
else
wfr_interpolation_order_ = interp_order;
}
}
void
nest::SimulationManager::simulate( Time const& t )
{
assert( kernel().is_initialized() );
t_real_ = 0;
t_slice_begin_ = timeval();
t_slice_end_ = timeval();
if ( t == Time::ms( 0.0 ) )
return;
if ( t < Time::step( 1 ) )
{
LOG( M_ERROR,
"SimulationManager::simulate",
String::compose( "Simulation time must be >= %1 ms (one time step).",
Time::get_resolution().get_ms() ) );
throw KernelException();
}
if ( t.is_finite() )
{
Time time1 = clock_ + t;
if ( !time1.is_finite() )
{
std::string msg = String::compose(
"A clock overflow will occur after %1 of %2 ms. Please reset network "
"clock first!",
( Time::max() - clock_ ).get_ms(),
t.get_ms() );
LOG( M_ERROR, "SimulationManager::simulate", msg );
throw KernelException();
}
}
else
{
std::string msg = String::compose(
"The requested simulation time exceeds the largest time NEST can handle "
"(T_max = %1 ms). Please use a shorter time!",
Time::max().get_ms() );
LOG( M_ERROR, "SimulationManager::simulate", msg );
throw KernelException();
}
to_do_ += t.get_steps();
to_do_total_ = to_do_;
const size_t num_active_nodes = prepare_simulation_();
// from_step_ is not touched here. If we are at the beginning
// of a simulation, it has been reset properly elsewhere. If
// a simulation was ended and is now continued, from_step_ will
// have the proper value. to_step_ is set as in advance_time().
delay end_sim = from_step_ + to_do_;
if ( kernel().connection_manager.get_min_delay() < end_sim )
to_step_ =
kernel()
.connection_manager.get_min_delay(); // update to end of time slice
else
to_step_ = end_sim; // update to end of simulation time
// Warn about possible inconsistencies, see #504.
// This test cannot come any earlier, because we first need to compute
// min_delay_
// above.
if ( t.get_steps() % kernel().connection_manager.get_min_delay() != 0 )
LOG( M_WARNING,
"SimulationManager::simulate",
"The requested simulation time is not an integer multiple of the minimal "
"delay in the network. This may result in inconsistent results under the "
"following conditions: (i) A network contains more than one source of "
"randomness, e.g., two different poisson_generators, and (ii) Simulate "
"is called repeatedly with simulation times that are not multiples of "
"the minimal delay." );
resume_( num_active_nodes );
finalize_simulation_();
}
void
nest::SimulationManager::set_status( const DictionaryDatum& d )
{
// Create an instance of time converter here to capture the current
// representation of time objects: TICS_PER_MS and TICS_PER_STEP
// will be stored in time_converter.
// This object can then be used to convert times in steps
// (e.g. Connection::delay_) or tics to the new representation.
// We pass this object to ConnectionManager::calibrate to update
// all time objects in the connection system to the new representation.
// MH 08-04-14
TimeConverter time_converter;
double_t time;
if ( updateValue< double_t >( d, "time", time ) )
{
if ( time != 0.0 )
throw BadProperty( "The simulation time can only be set to 0.0." );
if ( clock_ > TimeZero )
{
// reset only if time has passed
LOG( M_WARNING,
"SimulationManager::set_status",
"Simulation time reset to t=0.0. Resetting the simulation time is not "
"fully supported in NEST at present. Some spikes may be lost, and "
"stimulating devices may behave unexpectedly. PLEASE REVIEW YOUR "
"SIMULATION OUTPUT CAREFULLY!" );
clock_ = Time::step( 0 );
from_step_ = 0;
slice_ = 0;
kernel().event_delivery_manager.configure_spike_buffers(); // clear all old spikes
}
}
updateValue< bool >( d, "print_time", print_time_ );
// tics_per_ms and resolution must come after local_num_thread / total_num_threads
// because they might reset the network and the time representation
nest::double_t tics_per_ms;
bool tics_per_ms_updated = updateValue< nest::double_t >( d, "tics_per_ms", tics_per_ms );
double_t resd;
bool res_updated = updateValue< double_t >( d, "resolution", resd );
if ( tics_per_ms_updated || res_updated )
{
if ( kernel().node_manager.size() > 1 ) // root always exists
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Cannot change time representation after nodes have been created. Please call ResetKernel "
"first." );
throw KernelException();
}
else if ( has_been_simulated() ) // someone may have simulated empty network
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Cannot change time representation after the network has been simulated. Please call "
"ResetKernel first." );
throw KernelException();
}
else if ( kernel().connection_builder_manager.get_num_connections() != 0 )
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Cannot change time representation after connections have been created. Please call "
"ResetKernel first." );
throw KernelException();
}
else if ( res_updated
&& tics_per_ms_updated ) // only allow TICS_PER_MS to be changed together with resolution
{
if ( resd < 1.0 / tics_per_ms )
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Resolution must be greater than or equal to one tic. Value unchanged." );
throw KernelException();
}
else
{
nest::Time::set_resolution( tics_per_ms, resd );
clock_.calibrate(); // adjust to new resolution
// adjust delays in the connection system to new resolution
kernel().connection_builder_manager.calibrate( time_converter );
kernel().model_manager.calibrate( time_converter );
LOG( M_INFO, "SimulationManager::set_status", "tics per ms and resolution changed." );
}
}
else if ( res_updated ) // only resolution changed
{
if ( resd < Time::get_ms_per_tic() )
{
LOG( M_ERROR,
"SimulationManager::set_status",
"Resolution must be greater than or equal to one tic. Value unchanged." );
throw KernelException();
}
else
{
Time::set_resolution( resd );
clock_.calibrate(); // adjust to new resolution
// adjust delays in the connection system to new resolution
kernel().connection_builder_manager.calibrate( time_converter );
kernel().model_manager.calibrate( time_converter );
LOG( M_INFO, "SimulationManager::set_status", "Temporal resolution changed." );
}
}
else
{
LOG( M_ERROR,
"SimulationManager::set_status",
"change of tics_per_step requires simultaneous specification of resolution." );
throw KernelException();
}
}
// set the number of preliminary update cycles
// e.g. for the implementation of gap junctions
long nprelim;
if ( updateValue< long >( d, "max_num_prelim_iterations", nprelim ) )
{
if ( nprelim < 0 )
LOG( M_ERROR,
"SimulationManager::set_status",
"Number of preliminary update iterations must be zero or positive." );
else
max_num_prelim_iterations_ = nprelim;
}
double_t tol;
if ( updateValue< double_t >( d, "prelim_tol", tol ) )
{
if ( tol < 0.0 )
LOG( M_ERROR, "SimulationManager::set_status", "Tolerance must be zero or positive" );
else
prelim_tol_ = tol;
}
long interp_order;
if ( updateValue< long >( d, "prelim_interpolation_order", interp_order ) )
{
if ( ( interp_order < 0 ) || ( interp_order == 2 ) || ( interp_order > 3 ) )
LOG( M_ERROR, "SimulationManager::set_status", "Interpolation order must be 0, 1, or 3." );
else
prelim_interpolation_order_ = interp_order;
}
}
void
nest::SimulationManager::run( Time const& t )
{
assert_valid_simtime( t );
if ( not prepared_ )
{
std::string msg = "Run called without calling Prepare.";
LOG( M_ERROR, "SimulationManager::run", msg );
throw KernelException();
}
to_do_ += t.get_steps();
to_do_total_ = to_do_;
if ( to_do_ == 0 )
{
return;
}
// Reset profiling timers and counters within event_delivery_manager
kernel().event_delivery_manager.reset_timers_counters();
// Check whether waveform relaxation is used on any MPI process
kernel().node_manager.check_wfr_use();
// from_step_ is not touched here. If we are at the beginning
// of a simulation, it has been reset properly elsewhere. If
// a simulation was ended and is now continued, from_step_ will
// have the proper value. to_step_ is set as in advance_time().
delay end_sim = from_step_ + to_do_;
if ( kernel().connection_manager.get_min_delay() < end_sim )
{
to_step_ =
kernel()
.connection_manager.get_min_delay(); // update to end of time slice
}
else
{
to_step_ = end_sim; // update to end of simulation time
}
// Warn about possible inconsistencies, see #504.
// This test cannot come any earlier, because we first need to compute
// min_delay_
// above.
if ( t.get_steps() % kernel().connection_manager.get_min_delay() != 0 )
{
LOG( M_WARNING,
"SimulationManager::run",
"The requested simulation time is not an integer multiple of the minimal "
"delay in the network. This may result in inconsistent results under the "
"following conditions: (i) A network contains more than one source of "
"randomness, e.g., two different poisson_generators, and (ii) Simulate "
"is called repeatedly with simulation times that are not multiples of "
"the minimal delay." );
}
call_update_();
kernel().node_manager.post_run_cleanup();
}
void
nest::SimulationManager::prepare()
{
assert( kernel().is_initialized() );
if ( prepared_ )
{
std::string msg = "Prepare called twice.";
LOG( M_ERROR, "SimulationManager::prepare", msg );
throw KernelException();
}
if ( inconsistent_state_ )
{
throw KernelException(
"Kernel is in inconsistent state after an "
"earlier error. Please run ResetKernel first." );
}
t_real_ = 0;
t_slice_begin_ = timeval(); // set to timeval{0, 0} as unset flag
t_slice_end_ = timeval(); // set to timeval{0, 0} as unset flag
// find shortest and longest delay across all MPI processes
// this call sets the member variables
kernel().connection_manager.update_delay_extrema_();
kernel().event_delivery_manager.init_moduli();
// Check for synchronicity of global rngs over processes.
// We need to do this ahead of any simulation in case random numbers
// have been consumed on the SLI level.
if ( kernel().mpi_manager.get_num_processes() > 1 )
{
if ( not kernel().mpi_manager.grng_synchrony(
kernel().rng_manager.get_grng()->ulrand( 100000 ) ) )
{
LOG( M_ERROR,
"SimulationManager::prepare",
"Global Random Number Generators are not synchronized prior to "
"simulation." );
throw KernelException();
}
}
// if at the beginning of a simulation, set up spike buffers
if ( not simulated_ )
{
kernel().event_delivery_manager.configure_spike_buffers();
}
kernel().node_manager.ensure_valid_thread_local_ids();
kernel().node_manager.prepare_nodes();
kernel().model_manager.create_secondary_events_prototypes();
// we have to do enter_runtime after prepare_nodes, since we use
// calibrate to map the ports of MUSIC devices, which has to be done
// before enter_runtime
if ( not simulated_ ) // only enter the runtime mode once
{
double tick = Time::get_resolution().get_ms()
* kernel().connection_manager.get_min_delay();
kernel().music_manager.enter_runtime( tick );
}
prepared_ = true;
}
