Eigen::VectorXd DistributedDiff::diff(const unsigned long long &u_ts, const Eigen::VectorXd &samples) {
addDataToBuffer(u_ts, samples);
// Next we want to calculate all the differentials
Eigen::VectorXd diff_(size);
diff_ = FindDifferentials();
return diff_;
}
void GeneOntology::synchronize(){
// we received the response
if(m_inbox->hasMessage(RAY_MPI_TAG_SYNCHRONIZE_TERMS_REPLY)){
#ifdef DEBUG_ONTOLOGY_SYNC
cout<<"[DEBUG_ONTOLOGY_SYNC] Received RAY_MPI_TAG_SYNCHRONIZE_TERMS_REPLY"<<endl;
#endif
m_waitingForReply=false;
}
if(m_waitingForReply){
return;
}
bool isMaster=m_core->getRank() == MASTER_RANK;
if(!m_synchronizedTotal && !isMaster){
MessageUnit*buffer=(MessageUnit*)m_outboxAllocator->allocate(MAXIMUM_MESSAGE_SIZE_IN_BYTES);
int bufferPosition=0;
m_synchronizedTotal=true;
buffer[bufferPosition++]=SENTINEL_VALUE_FOR_TOTAL;
buffer[bufferPosition++]=SENTINEL_VALUE_FOR_TOTAL;
buffer[bufferPosition++]=m_kmerObservationsWithGeneOntologies;
m_switchMan->sendMessage(buffer,bufferPosition,m_outbox,m_rank,MASTER_RANK,RAY_MPI_TAG_SYNCHRONIZE_TERMS);
m_waitingForReply=true;
return;
}
// sync with master
if(hasDataToSync() && !isMaster){
#ifdef DEBUG_ONTOLOGY_SYNC
cout<<"[DEBUG_ONTOLOGY_SYNC] Will create data message"<<endl;
#endif
MessageUnit*buffer=(MessageUnit*)m_outboxAllocator->allocate(MAXIMUM_MESSAGE_SIZE_IN_BYTES);
#ifdef ASSERT
assert(buffer!=NULL);
#endif
int bufferPosition=0;
int available=(MAXIMUM_MESSAGE_SIZE_IN_BYTES/sizeof(MessageUnit))/3;
int added=0;
while(hasDataToSync() && added < available){
#ifdef DEBUG_ONTOLOGY_SYNC
cout<<"[DEBUG_ONTOLOGY_SYNC] will add an object."<<endl;
#endif
#ifdef ASSERT
if(added==0){
assert(bufferPosition==0);
}
#endif
addDataToBuffer(buffer,&bufferPosition);
#ifdef ASSERT
assert(bufferPosition%3 == 0);
#endif
added++;
#ifdef DEBUG_ONTOLOGY_SYNC
cout<<"[DEBUG_ONTOLOGY_SYNC] added "<<added<<" available "<<available<<endl;
#endif
}
#ifdef DEBUG_ONTOLOGY_SYNC
cout<<"[DEBUG_ONTOLOGY_SYNC] sending RAY_MPI_TAG_SYNCHRONIZE_TERMS"<<endl;
#endif
m_switchMan->sendMessage(buffer,bufferPosition,m_outbox,m_rank,MASTER_RANK,RAY_MPI_TAG_SYNCHRONIZE_TERMS);
m_waitingForReply=true;
}
/* we are not waiting for a reply and we don't have more data to synchronize */
if(!m_waitingForReply){
m_synced=true;
cout<<"Rank "<<m_rank<<": synced ontology term profiles with master"<<endl;
m_switchMan->sendMessage(NULL,0,m_outbox,m_rank,MASTER_RANK,RAY_MPI_TAG_SYNCHRONIZATION_DONE);
}
}
void DocBookBookReader::characterDataHandler(const char *text, std::size_t len) {
addDataToBuffer(text, len);
}
