//bool AttributeContainer::hasAttribute(const std::string &name)
//{
// return m_attributes.exists(name);
//}
AttributeContainer::AttributeContainer(const AttributeContainer &container)
{
std::vector<std::string> keys=container.keys();
for(size_t i=0; i<keys.size(); ++i)
{
addAttribute(container.attribute(keys[i]));
}
}
void SyncBuffer::pop(SpikeDelay * delay, NeuronID size)
{
for (NeuronID i = 1 ; i < MINDELAY+1 ; ++i ) {
delay->get_spikes(i)->clear();
delay->get_spikes(i)->clear();
}
for (int r = 0 ; r < mpicom->size() ; ++r ) {
NeuronID numberOfSpikes = recv_buf[r*max_send_size]; // total data
NeuronID * iter = &recv_buf[r*max_send_size+pop_offsets[r]]; // first spike
NeuronID temp = (*iter - groupPopOffset);
NeuronID spike = temp%size; // spike (if it exists) in current group
int t = temp/size; // timeslice in MINDELAY if we are out this might be the next group
for ( int i = 0 ; i < MINDELAY ; ++i ) count[i] = 0;
// while we are in the current group && have not read all entries
while ( t < MINDELAY && numberOfSpikes ) {
delay->get_spikes(t+1)->push_back(spike);
iter++;
numberOfSpikes--;
count[t]++; // store spike counts for each time-slice
temp = (*iter - groupPopOffset);
spike = temp%size;
t = temp/size;
}
// extract a total of count*get_num_attributes() attributes
if ( delay->get_num_attributes() ) {
for ( NeuronID slice = 0 ; slice < MINDELAY ; ++slice ) {
AttributeContainer * ac = delay->get_attributes(slice+1);
for ( NeuronID k = 0 ; k < delay->get_num_attributes() ; ++k ) { // loop over attributes
for ( NeuronID s = 0 ; s < count[slice] ; ++s ) { // loop over spikes
AurynFloat * attrib;
attrib = (AurynFloat*)(iter);
iter++;
ac->push_back(*attrib);
// if ( mpicom->rank() == 0 )
// cout << " reading attr " << " " << slice << " " << k << " " << s << " " << scientific << *attrib << endl;
}
}
}
}
recv_buf[r*max_send_size] = numberOfSpikes; // save remaining entries
pop_offsets[r] = iter - &recv_buf[r*max_send_size]; // save offset in recv_buf section
}
groupPopOffset += size*MINDELAY;
}
void SyncBuffer::push(SpikeDelay * delay, const NeuronID size)
{
// DEBUG
// std::cout << "Rank " << mpicom->rank() << "push\n";
// delay->print();
const SYNCBUFFER_DELTA_DATATYPE grid_size = (SYNCBUFFER_DELTA_DATATYPE)size*MINDELAY;
SYNCBUFFER_DELTA_DATATYPE unrolled_last_pos = 0;
// circular loop over different delay bins
for (int slice = 0 ; slice < MINDELAY ; ++slice ) {
SpikeContainer * sc = delay->get_spikes(slice+1);
AttributeContainer * ac = delay->get_attributes(slice+1);
// loop over all spikes in current delay time slice
for (int i = 0 ;
i < sc->size() ;
++i ) {
NeuronID spike = sc->at(i);
// compute unrolled position in current delay
SYNCBUFFER_DELTA_DATATYPE unrolled_pos = (SYNCBUFFER_DELTA_DATATYPE)(spike) + (SYNCBUFFER_DELTA_DATATYPE)size*slice;
// compute vertical unrolled difference from last spike
SYNCBUFFER_DELTA_DATATYPE spike_delta = unrolled_pos + carry_offset - unrolled_last_pos;
// memorize current position in slice
unrolled_last_pos = unrolled_pos;
// discard carry_offset since its only added to the first spike_delta
carry_offset = 0;
// overflow managment -- should only ever kick in for very very large SpikingGroups and very very sparse activity
while ( spike_delta >= max_delta_size ) {
send_buf.push_back( max_delta_size );
spike_delta -= max_delta_size;
}
// storing the spike delta (or its remainder) to buffer
send_buf.push_back(spike_delta);
// append spike attributes here in buffer
for ( int k = 0 ; k < delay->get_num_attributes() ; ++k ) { // loop over attributes
NeuronID cast_attrib = *(NeuronID*)(&(ac->at(i*delay->get_num_attributes()+k)));
send_buf.push_back(cast_attrib);
// std::cout << "store " << std::scientific << ac->at(i*delay->get_num_attributes()+k) << " int " << cast_attrib << std::endl;
}
}
}
// set save carry_offset which is the remaining difference from the present group
// plus because there might be more than one group without a spike ...
carry_offset += grid_size-unrolled_last_pos;
}
void SyncBuffer::push(SpikeDelay * delay, NeuronID size)
{
for (NeuronID i = 1 ; i < MINDELAY+1 ; ++i ) {
SpikeContainer * sc = delay->get_spikes(i);
// NeuronID s = (NeuronID) (sc->size());
// send_buf[0] += s;
count[i-1] = 0;
for (SpikeContainer::const_iterator spike = sc->begin() ;
spike != sc->end() ; ++spike ) {
NeuronID compressed = *spike + groupPushOffset1 + (i-1)*size;
send_buf.push_back(compressed);
count[i-1]++;
}
send_buf[0] += delay->get_spikes(i)->size(); // send the total number of spikes
}
// transmit get_num_attributes() attributes for count spikes for all time slices
if ( delay->get_num_attributes() ) {
for (NeuronID i = 1 ; i < MINDELAY+1 ; ++i ) {
AttributeContainer * ac = delay->get_attributes(i);
for ( NeuronID k = 0 ; k < delay->get_num_attributes() ; ++k ) { // loop over attributes
for ( NeuronID s = 0 ; s < count[i-1] ; ++s ) { // loop over spikes
send_buf.push_back(*(NeuronID*)(&(ac->at(s+count[i-1]*k))));
// if ( mpicom->rank() == 0 )
// cout << " pushing attr " << " " << i << " " << k << " " << s << " "
// << scientific << ac->at(s+count[i-1]*k) << endl;
}
}
}
}
groupPushOffset1 += size*MINDELAY;
}
void foreach_attrib(AttributeContainer& attr_cont, std::vector<FunctorAttribThreaded*> funcs)
{
unsigned int nbth = funcs.size();
std::vector<unsigned int >* vid = new std::vector<unsigned int>[2*nbth];
boost::thread** threads = new boost::thread*[nbth];
for (unsigned int i = 0; i < 2*nbth; ++i)
vid[i].reserve(SIZE_BUFFER_THREAD);
// fill each vid buffers with 4096 id
unsigned int id = attr_cont.begin();
unsigned int nb = 0;
unsigned int nbm = nbth*SIZE_BUFFER_THREAD;
while ((id != attr_cont.end()) && (nb < nbm))
{
vid[nb%nbth].push_back(id);
nb++;
attr_cont.next(id);
}
boost::barrier sync1(nbth+1);
boost::barrier sync2(nbth+1);
bool finished=false;
// lauch threads
for (unsigned int i = 0; i < nbth; ++i)
threads[i] = new boost::thread(ThreadFunctionAttrib(funcs[i], vid[i],sync1,sync2, finished,1+i));
while (id != attr_cont.end())
{
for (unsigned int i = nbth; i < 2*nbth; ++i)
vid[i].clear();
unsigned int nb = 0;
while ((id != attr_cont.end()) && (nb < nbm))
{
vid[nbth + nb%nbth].push_back(id);
nb++;
attr_cont.next(id);
}
sync1.wait();
for (unsigned int i = 0; i < nbth; ++i)
vid[i].swap(vid[nbth+i]);
sync2.wait();
}
sync1.wait();
finished = true;
sync2.wait();
//wait for all theads to be finished
for (unsigned int i = 0; i < nbth; ++i)
{
threads[i]->join();
delete threads[i];
}
delete[] threads;
delete[] vid;
}
