void HostMatrix::updateSize(int numberOfRows, int numberOfColumns) {
#ifdef DEBUG
if(numberOfRows > numberOfRealRows){
throw DimensionMismatch("Number of rows for HostMatrix can't be larger than the real number of rows.");
}
if(numberOfColumns > numberOfRealColumns){
throw DimensionMismatch("Number of columns for HostMatrix can't be larger than the real number of columns.");
}
#endif
this->numberOfRows = numberOfRows;
this->numberOfColumns = numberOfColumns;
}
void cg_connect(ConnectionGeneratorDatum& cg, RangeSet& sources, std::vector<long>& source_gids, RangeSet& targets, std::vector<long>& target_gids, DictionaryDatum params_map, index syn)
{
cg_set_masks(cg, sources, targets);
cg->start();
int source, target, num_parameters = cg->arity();
if (num_parameters == 0)
{
while (cg->next(source, target, NULL))
ConnectionGeneratorModule::get_network().connect(source_gids.at(source), target_gids.at(target), syn);
}
else if (num_parameters == 2)
{
if (!params_map->known(names::weight) || !params_map->known(names::delay))
throw BadProperty("The parameter map has to contain the indices of weight and delay.");
long w_idx = (*params_map)[names::weight];
long d_idx = (*params_map)[names::delay];
std::vector<double> params(2);
while (cg->next(source, target, ¶ms[0]))
ConnectionGeneratorModule::get_network().connect(source_gids.at(source), target_gids.at(target), params[w_idx], params[d_idx], syn);
}
else
{
ConnectionGeneratorModule::get_network().message(SLIInterpreter::M_ERROR, "Connect", "Either two or no parameters in the Connection Set expected.");
throw DimensionMismatch();
}
}
HostMatrix::HostMatrix(int numberOfRealRows, int numberOfRealColumns, int numberOfRows, int numberOfColumns,
PRECISION* hostMatrix) :
numberOfRealRows(numberOfRealRows), numberOfRealColumns(numberOfRealColumns), numberOfRows(numberOfRows), numberOfColumns(
numberOfColumns), hostMatrix(hostMatrix) {
if(numberOfRows <= 0 || numberOfColumns <= 0 || numberOfRealRows <= 0 || numberOfRealColumns <= 0){
throw DimensionMismatch("Number of rows and columns for HostMatrix must be > 0");
}
}
void
cg_connect( ConnectionGeneratorDatum& cg,
RangeSet& sources,
std::vector< long >& source_gids,
RangeSet& targets,
std::vector< long >& target_gids,
DictionaryDatum params_map,
index syn )
{
cg_set_masks( cg, sources, targets );
cg->start();
int source, target, num_parameters = cg->arity();
if ( num_parameters == 0 )
{
// connect source to target
while ( cg->next( source, target, NULL ) )
{
if ( kernel().node_manager.is_local_gid( target_gids.at( target ) ) )
{
Node* const target_node = kernel().node_manager.get_node( target_gids.at( target ) );
const thread target_thread = target_node->get_thread();
kernel().connection_builder_manager.connect(
source_gids.at( source ), target_node, target_thread, syn );
}
}
}
else if ( num_parameters == 2 )
{
if ( !params_map->known( names::weight ) || !params_map->known( names::delay ) )
throw BadProperty( "The parameter map has to contain the indices of weight and delay." );
long w_idx = ( *params_map )[ names::weight ];
long d_idx = ( *params_map )[ names::delay ];
std::vector< double > params( 2 );
// connect source to target with weight and delay
while ( cg->next( source, target, ¶ms[ 0 ] ) )
{
if ( kernel().node_manager.is_local_gid( target_gids.at( target ) ) )
{
Node* const target_node = kernel().node_manager.get_node( target_gids.at( target ) );
const thread target_thread = target_node->get_thread();
kernel().connection_builder_manager.connect( source_gids.at( source ),
target_node,
target_thread,
syn,
params[ d_idx ],
params[ w_idx ] );
}
}
}
else
{
LOG( M_ERROR, "Connect", "Either two or no parameters in the Connection Set expected." );
throw DimensionMismatch();
}
}
/**
* Solves the disconnection of two nodes on a OneToOne basis without
* structural plasticity. This means this method can be manually called
* by the user to delete existing synapses.
*/
void
nest::OneToOneBuilder::disconnect_()
{
// make sure that target and source population have the same size
if ( sources_->size() != targets_->size() )
{
LOG( M_ERROR,
"Disconnect",
"Source and Target population must be of the same size." );
throw DimensionMismatch();
}
#pragma omp parallel
{
// get thread id
const int tid = kernel().vp_manager.get_thread_id();
try
{
for ( GIDCollection::const_iterator tgid = targets_->begin(),
sgid = sources_->begin();
tgid != targets_->end();
++tgid, ++sgid )
{
assert( sgid != sources_->end() );
// check whether the target is on this mpi machine
if ( not kernel().node_manager.is_local_gid( *tgid ) )
{
skip_conn_parameter_( tid );
continue;
}
Node* const target = kernel().node_manager.get_node( *tgid );
const thread target_thread = target->get_thread();
// check whether the target is on our thread
if ( tid != target_thread )
{
skip_conn_parameter_( tid );
continue;
}
single_disconnect_( *sgid, *target, target_thread );
}
}
catch ( std::exception& err )
{
// We must create a new exception here, err's lifetime ends at
// the end of the catch block.
exceptions_raised_.at( tid ) =
lockPTR< WrappedThreadException >( new WrappedThreadException( err ) );
}
}
}
/**
* In charge of dynamically creating the new synapses
* @param sources nodes from which synapses can be created
* @param targets target nodes for the newly created synapses
*/
void
nest::SPBuilder::connect_( GIDCollection sources, GIDCollection targets )
{
// Code copied and adapted from OneToOneBuilder::connect_()
// make sure that target and source population have the same size
if ( sources.size() != targets.size() )
{
LOG( M_ERROR,
"Connect",
"Source and Target population must be of the same size." );
throw DimensionMismatch();
}
#pragma omp parallel
{
// get thread id
const int tid = kernel().vp_manager.get_thread_id();
try
{
// allocate pointer to thread specific random generator
librandom::RngPtr rng = kernel().rng_manager.get_rng( tid );
for ( GIDCollection::const_iterator tgid = targets.begin(),
sgid = sources.begin();
tgid != targets.end();
++tgid, ++sgid )
{
assert( sgid != sources.end() );
if ( *sgid == *tgid and not autapses_ )
continue;
if ( !change_connected_synaptic_elements( *sgid, *tgid, tid, 1 ) )
{
skip_conn_parameter_( tid );
continue;
}
Node* const target = kernel().node_manager.get_node( *tgid );
const thread target_thread = target->get_thread();
single_connect_( *sgid, *target, target_thread, rng );
}
}
catch ( std::exception& err )
{
// We must create a new exception here, err's lifetime ends at
// the end of the catch block.
exceptions_raised_.at( tid ) =
lockPTR< WrappedThreadException >( new WrappedThreadException( err ) );
}
}
}
void nest::ac_poisson_generator::init_buffers_()
{
device_.init_buffers();
B_.rates_.clear_data();
B_.N_osc_ = P_.om_.size();
if ( ! ( P_.ac_.size() == B_.N_osc_ && P_.phi_.size() == B_.N_osc_ ) )
{
network()->message(SLIInterpreter::M_ERROR,
"ac_poisson_generator::calibrate",
"Frequency, AC amplitude, and phase arrays "
"must have equal size!");
throw DimensionMismatch();
}
/* state vector:
- dc component is constant and not included
- rate is accumulated directly in update
- vector contains two elements for each oscillator
*/
B_.state_oscillators_.resize(2*B_.N_osc_, 0);
// remaining elements, see Rotter & Diesmann, 3.1.3
// phi = pi/2 is stable, since tan(phi)^2 appears in denominator only
// assumes IEEE arithmetic with 1/Inf = 0
// sign is handled below when assigning to S_
const std::valarray<double_t> q =
P_.ac_ / std::sqrt(1.0 + std::pow(std::tan(P_.phi_), 2.0));
// valarray slices do not appear to be reliable under Tru64 CXX,
// so one better uses for loops.
for ( size_t n = 0 ; n < B_.N_osc_ ; ++n )
{
B_.state_oscillators_[2 * n ] =
std::cos(P_.phi_[n]) >= 0 ? q[n] : -q[n];
B_.state_oscillators_[2 * n + 1] = std::sin(P_.phi_[n]) >= 0
? std::sqrt(std::pow(P_.ac_[n],2.0)-std::pow(q[n],2.0))
: -std::sqrt(std::pow(P_.ac_[n],2.0)-std::pow(q[n],2.0));
}
}
DataLocation<Matrix, Vector>::DataLocation(Vector* snpVector, Vector* environmentVector, Vector* interactionVector,
Vector* phenotypeVector, Matrix* covariatesMatrix) :
snpVector(snpVector), environmentVector(environmentVector), interactionVector(interactionVector), phenotypeVector(
phenotypeVector), covariatesMatrix(covariatesMatrix){
#ifdef DEBUG
int sLength = snpVector.getRealNumberOfRows();
int eLength = environmentVector.getRealNumberOfRows();
int iLength = interactionVector.getRealNumberOfRows();
int pLength = phenotypeVector.getRealNumberOfRows();
int cLength = covariatesMatrix.getRealNumberOfRows();
if(sLength != eLength || sLength != iLength || sLength != pLength || sLength != cLength){
std::ostringstream os;
os << "DataLocation number of rows of containers does not match" << std::endl;
const std::string& tmp = os.str();
throw DimensionMismatch(tmp.c_str());
}
#endif
}
void
nest::RNGManager::set_status( const DictionaryDatum& d )
{
// have those two for later asking, whether threads have changed:
long n_threads;
bool n_threads_updated =
updateValue< long >( d, "local_num_threads", n_threads );
// set RNGs --- MUST come after n_threads_ is updated
if ( d->known( "rngs" ) )
{
// this array contains pre-seeded RNGs, so they can be used
// directly, no seeding required
ArrayDatum* ad = dynamic_cast< ArrayDatum* >( ( *d )[ "rngs" ].datum() );
if ( ad == 0 )
throw BadProperty();
// n_threads_ is the new value after a change of the number of
// threads
if ( ad->size()
!= ( size_t )( kernel().vp_manager.get_num_virtual_processes() ) )
{
LOG( M_ERROR,
"RNGManager::set_status",
"Number of RNGs must equal number of virtual processes "
"(threads*processes). RNGs "
"unchanged." );
throw DimensionMismatch(
( size_t )( kernel().vp_manager.get_num_virtual_processes() ),
ad->size() );
}
// delete old generators, insert new generators this code is
// robust under change of thread number in this call to
// set_status, as long as it comes AFTER n_threads_ has been
// upated
rng_.clear();
for ( index i = 0; i < ad->size(); ++i )
if ( kernel().vp_manager.is_local_vp( i ) )
rng_.push_back( getValue< librandom::RngDatum >(
( *ad )[ kernel().vp_manager.suggest_vp( i ) ] ) );
}
else if ( n_threads_updated && kernel().node_manager.size() == 0 )
{
LOG( M_WARNING,
"RNGManager::set_status",
"Equipping threads with new default RNGs" );
create_rngs_();
}
if ( d->known( "rng_seeds" ) )
{
ArrayDatum* ad =
dynamic_cast< ArrayDatum* >( ( *d )[ "rng_seeds" ].datum() );
if ( ad == 0 )
throw BadProperty();
if ( ad->size()
!= ( size_t )( kernel().vp_manager.get_num_virtual_processes() ) )
{
LOG( M_ERROR,
"RNGManager::set_status",
"Number of seeds must equal number of virtual processes "
"(threads*processes). RNGs unchanged." );
throw DimensionMismatch(
( size_t )( kernel().vp_manager.get_num_virtual_processes() ),
ad->size() );
}
// check if seeds are unique
std::set< ulong_t > seedset;
for ( index i = 0; i < ad->size(); ++i )
{
long s = ( *ad )[ i ]; // SLI has no ulong tokens
if ( !seedset.insert( s ).second )
{
LOG( M_WARNING,
"RNGManager::set_status",
"Seeds are not unique across threads!" );
break;
}
}
// now apply seeds, resets generators automatically
for ( index i = 0; i < ad->size(); ++i )
{
long s = ( *ad )[ i ];
if ( kernel().vp_manager.is_local_vp( i ) )
rng_[ kernel().vp_manager.vp_to_thread(
kernel().vp_manager.suggest_vp( i ) ) ]->seed( s );
rng_seeds_[ i ] = s;
}
} // if rng_seeds
// set GRNG
if ( d->known( "grng" ) )
{
// pre-seeded grng that can be used directly, no seeding required
updateValue< librandom::RngDatum >( d, "grng", grng_ );
}
else if ( n_threads_updated && kernel().node_manager.size() == 0 )
{
LOG( M_WARNING,
"RNGManager::set_status",
"Equipping threads with new default GRNG" );
create_grng_();
}
if ( d->known( "grng_seed" ) )
{
const long gseed = getValue< long >( d, "grng_seed" );
// check if grng seed is unique with respect to rng seeds
// if grng_seed and rng_seeds given in one SetStatus call
std::set< ulong_t > seedset;
seedset.insert( gseed );
if ( d->known( "rng_seeds" ) )
{
ArrayDatum* ad_rngseeds =
dynamic_cast< ArrayDatum* >( ( *d )[ "rng_seeds" ].datum() );
if ( ad_rngseeds == 0 )
throw BadProperty();
for ( index i = 0; i < ad_rngseeds->size(); ++i )
{
const long vpseed = ( *ad_rngseeds )[ i ]; // SLI has no ulong tokens
if ( !seedset.insert( vpseed ).second )
{
LOG( M_WARNING,
"RNGManager::set_status",
"Seeds are not unique across threads!" );
break;
}
}
}
// now apply seed, resets generator automatically
grng_seed_ = gseed;
grng_->seed( gseed );
} // if grng_seed
}
void
cg_connect( ConnectionGeneratorDatum& cg,
RangeSet& sources,
index source_offset,
RangeSet& targets,
index target_offset,
DictionaryDatum params_map,
index syn )
{
cg_set_masks( cg, sources, targets );
cg->start();
int source, target, num_parameters = cg->arity();
if ( num_parameters == 0 )
{
// connect source to target
while ( cg->next( source, target, NULL ) )
{
if ( ConnectionGeneratorModule::get_network().is_local_gid( target + target_offset ) )
{
Node* const target_node =
ConnectionGeneratorModule::get_network().get_node( target + target_offset );
const thread target_thread = target_node->get_thread();
ConnectionGeneratorModule::get_network().connect(
source + source_offset, target_node, target_thread, syn );
}
}
}
else if ( num_parameters == 2 )
{
if ( !params_map->known( names::weight ) || !params_map->known( names::delay ) )
throw BadProperty( "The parameter map has to contain the indices of weight and delay." );
long w_idx = ( *params_map )[ names::weight ];
long d_idx = ( *params_map )[ names::delay ];
std::vector< double > params( 2 );
// connect source to target with weight and delay
while ( cg->next( source, target, ¶ms[ 0 ] ) )
{
if ( ConnectionGeneratorModule::get_network().is_local_gid( target + target_offset ) )
{
Node* const target_node =
ConnectionGeneratorModule::get_network().get_node( target + target_offset );
const thread target_thread = target_node->get_thread();
ConnectionGeneratorModule::get_network().connect( source + source_offset,
target_node,
target_thread,
syn,
params[ d_idx ],
params[ w_idx ] );
}
}
}
else
{
ConnectionGeneratorModule::get_network().message( SLIInterpreter::M_ERROR,
"Connect",
"Either two or no parameters in the Connection Set expected." );
throw DimensionMismatch();
}
}