void VertexMessenger::work(){
if(m_isDone){
return;
}else if(!m_requestedBasicInfo){
m_requestedBasicInfo=true;
m_receivedBasicInfo=false;
uint64_t*message=(uint64_t*)m_outboxAllocator->allocate(3*sizeof(uint64_t));
int j=0;
m_vertex.pack(message,&j);
message[j++]=m_waveId;
message[j++]=m_wavePosition;
Message aMessage(message,j,m_destination,RAY_MPI_TAG_VERTEX_INFO,m_parameters->getRank());
m_outbox->push_back(aMessage);
}else if(!m_receivedBasicInfo &&m_inbox->size()==1&&m_inbox->at(0)->getTag()==RAY_MPI_TAG_VERTEX_INFO_REPLY){
m_receivedBasicInfo=true;
uint64_t*buffer=(uint64_t*)m_inbox->at(0)->getBuffer();
m_coverageValue=buffer[0];
m_edges=buffer[1];
m_numberOfAnnotations=buffer[2];
m_pointer=(void*)buffer[3];
int numberOfReadsInMessage=buffer[4];
int i=0;
while(i<numberOfReadsInMessage){
int theRank=buffer[5+4*i];
int index=buffer[5+4*i+1];
int strandPosition=buffer[5+4*i+2];
char strand=buffer[5+4*i+3];
#ifdef ASSERT
assert(theRank>=0);
if(theRank>=m_parameters->getSize()){
cout<<"Rank="<<theRank<<" Size="<<m_parameters->getSize()<<endl;
}
assert(theRank<m_parameters->getSize());
assert(strand=='F'||strand=='R');
#endif
ReadAnnotation e;
e.constructor(theRank,index,strandPosition,strand,false);
m_annotations.push_back(e);
i++;
}
if(m_pointer==NULL){
m_isDone=true;
}else{
m_requestedReads=false;
m_mateIterator=m_matesToMeet->begin();
}
}else if(m_receivedBasicInfo){
if(m_coverageValue>=3*m_parameters->getPeakCoverage()){
getReadsForRepeatedVertex();
}else{
getReadsForUniqueVertex();
}
}
}
void VertexMessenger::getReadsForRepeatedVertex(){
if(!m_requestedReads){
uint64_t*message=(uint64_t*)m_outboxAllocator->allocate(MAXIMUM_MESSAGE_SIZE_IN_BYTES);
int j=0;
m_vertex.pack(message,&j);
message[j++]=(uint64_t)m_pointer;
int maximumMates=MAXIMUM_MESSAGE_SIZE_IN_BYTES/sizeof(uint64_t)/4;
int processed=0;
while(processed<maximumMates&&m_mateIterator!=m_matesToMeet->end()){
uint64_t mate=*m_mateIterator;
message[j+1+processed]=mate;
processed++;
m_mateIterator++;
}
message[j]=processed;
/*
* <--vertex--><--pointer--><--numberOfMates--><--mates -->
*/
Message aMessage(message,j+1+processed,
m_destination,RAY_MPI_TAG_VERTEX_READS_FROM_LIST,m_parameters->getRank());
m_outbox->push_back(aMessage);
m_requestedReads=true;
m_receivedReads=false;
}else if(!m_receivedReads&&m_inbox->size()==1&&m_inbox->at(0)->getTag()==RAY_MPI_TAG_VERTEX_READS_FROM_LIST_REPLY){
m_receivedReads=true;
uint64_t*buffer=(uint64_t*)m_inbox->at(0)->getBuffer();
int numberOfReadsInMessage=buffer[0];
int i=0;
while(i<numberOfReadsInMessage){
int theRank=buffer[1+4*i];
int index=buffer[1+4*i+1];
int strandPosition=buffer[1+4*i+2];
char strand=buffer[1+4*i+3];
#ifdef ASSERT
assert(theRank>=0);
if(theRank>=m_parameters->getSize()){
cout<<"Rank="<<theRank<<" Size="<<m_parameters->getSize()<<endl;
}
assert(theRank<m_parameters->getSize());
assert(strand=='F'||strand=='R');
#endif
ReadAnnotation e;
e.constructor(theRank,index,strandPosition,strand,false);
m_annotations.push_back(e);
i++;
}
if(m_mateIterator==m_matesToMeet->end()){
m_isDone=true;
}else{
m_requestedReads=false;
}
}
}
void ReadFetcher::work(){
if(m_done){
return;
}
if(!m_readsRequested){
uint64_t*message2=(uint64_t*)m_outboxAllocator->allocate(MAXIMUM_MESSAGE_SIZE_IN_BYTES);
int bufferPosition=0;
m_vertex.pack(message2,&bufferPosition);
message2[bufferPosition++]=(uint64_t)m_pointer;
int destination=m_parameters->_vertexRank(&m_vertex);
Message aMessage(message2,bufferPosition,destination,RAY_MPI_TAG_REQUEST_VERTEX_READS,m_parameters->getRank());
m_virtualCommunicator->pushMessage(m_workerId,&aMessage);
m_readsRequested=true;
}else if(m_virtualCommunicator->isMessageProcessed(m_workerId)){
vector<uint64_t> buffer;
m_virtualCommunicator->getMessageResponseElements(m_workerId,&buffer);
#ifdef ASSERT
assert((int)buffer.size()==5);
#endif
m_pointer=(void*)buffer[0];
int rank=buffer[1];
if(rank!=INVALID_RANK){
#ifdef ASSERT
if(!(rank>=0&&rank<m_parameters->getSize())){
cout<<"Error rank="<<rank<<endl;
cout<<"Buffer: ";
for(int i=0;i<5;i++){
cout<<buffer[i]<<" ";
}
cout<<endl;
}
assert(rank>=0&&rank<m_parameters->getSize());
#endif
ReadAnnotation readAnnotation;
readAnnotation.constructor(rank,buffer[2],buffer[3],buffer[4],false);
m_reads.push_back(readAnnotation);
}
if(m_pointer==NULL){
m_done=true;
}else{
uint64_t*message2=(uint64_t*)m_outboxAllocator->allocate(MAXIMUM_MESSAGE_SIZE_IN_BYTES);
int bufferPosition=0;
m_vertex.pack(message2,&bufferPosition);
message2[bufferPosition++]=(uint64_t)m_pointer;
int destination=m_parameters->_vertexRank(&m_vertex);
Message aMessage(message2,bufferPosition,destination,RAY_MPI_TAG_REQUEST_VERTEX_READS,m_parameters->getRank());
m_virtualCommunicator->pushMessage(m_workerId,&aMessage);
}
}
}
void VertexMessenger::getReadsForUniqueVertex(){
if(!m_requestedReads){
uint64_t*message=(uint64_t*)m_outboxAllocator->allocate(2*sizeof(uint64_t));
int j=0;
m_vertex.pack(message,&j);
message[j++]=(uint64_t)m_pointer;
Message aMessage(message,j,m_destination,RAY_MPI_TAG_VERTEX_READS,m_parameters->getRank());
m_outbox->push_back(aMessage);
m_requestedReads=true;
m_receivedReads=false;
}else if(!m_receivedReads&&m_inbox->size()==1&&m_inbox->at(0)->getTag()==RAY_MPI_TAG_VERTEX_READS_REPLY){
m_receivedReads=true;
uint64_t*buffer=(uint64_t*)m_inbox->at(0)->getBuffer();
int numberOfReadsInMessage=buffer[0];
int i=0;
while(i<numberOfReadsInMessage){
int theRank=buffer[1+4*i];
int index=buffer[1+4*i+1];
int strandPosition=buffer[1+4*i+2];
char strand=buffer[1+4*i+3];
#ifdef ASSERT
assert(theRank>=0);
if(theRank>=m_parameters->getSize()){
cout<<"Rank="<<theRank<<" Size="<<m_parameters->getSize()<<endl;
}
assert(theRank<m_parameters->getSize());
assert(strand=='F'||strand=='R');
#endif
ReadAnnotation e;
e.constructor(theRank,index,strandPosition,strand,false);
m_annotations.push_back(e);
i++;
}
m_pointer=(void*)buffer[1+numberOfReadsInMessage*4];
if((int)m_annotations.size()==m_numberOfAnnotations){
m_isDone=true;
}else{
m_requestedReads=false;
}
}
}
void ValueAnnotation:: register_annot()
{
ReadAnnotation* op = ReadAnnotation::get_inst();
op->add_TypeCollection( &values);
op->add_OperatorCollection(&valueRestrict);
}
void ReadFetcher::work() {
if(m_done) {
return;
}
if(!m_readsRequested) {
MessageUnit*message2=(MessageUnit*)m_outboxAllocator->allocate(MAXIMUM_MESSAGE_SIZE_IN_BYTES);
#ifdef CONFIG_ASSERT
assert(message2 != NULL);
#endif
int bufferPosition=0;
m_vertex.pack(message2,&bufferPosition);
MessageUnit integerValue=pack_pointer((void**)&m_pointer);
// fancy trick to transmit a void* over the network
message2[bufferPosition++]=integerValue;
int period=m_virtualCommunicator->getElementsPerQuery(RAY_MPI_TAG_REQUEST_VERTEX_READS);
// do some padding
while(bufferPosition<period) {
#ifdef CONFIG_ASSERT
assert(bufferPosition * sizeof(MessageUnit) < MAXIMUM_MESSAGE_SIZE_IN_BYTES);
#endif
message2[bufferPosition++]=0;
}
#ifdef CONFIG_ASSERT
int start=KMER_U64_ARRAY_SIZE+1;
assert(period>=5);
// Padding must be 0.
while(start<period) {
if(message2[start]!=0) {
cout<<"Error, padding must be 0."<<endl;
}
assert(message2[start]==0);
start++;
}
#endif
int destination=m_parameters->vertexRank(&m_vertex);
#ifdef GUILLIMIN_BUG
if(m_parameters->getRank()==destination) {
cout<<endl;
cout<<"worker: "<<m_workerId<<endl;
cout<<"Sending9 RAY_MPI_TAG_REQUEST_VERTEX_READS ptr="<<m_pointer<<" ";
cout<<" integerValue= "<<integerValue<<" to "<<destination<<endl;
for(int i=0; i<period; i++)
cout<<" "<<i<<" -> "<<message2[i];
cout<<endl;
}
#endif
Message aMessage(message2,period,destination,RAY_MPI_TAG_REQUEST_VERTEX_READS,
m_parameters->getRank());
m_virtualCommunicator->pushMessage(m_workerId,&aMessage);
m_readsRequested=true;
} else if(m_virtualCommunicator->isMessageProcessed(m_workerId)) {
vector<MessageUnit> buffer;
m_virtualCommunicator->getMessageResponseElements(m_workerId,&buffer);
#ifdef CONFIG_ASSERT
int period=m_virtualCommunicator->getElementsPerQuery(RAY_MPI_TAG_REQUEST_VERTEX_READS);
assert((int)buffer.size()==period);
#endif
//. ------
#ifdef GUILLIMIN_BUG
int destination=m_parameters->vertexRank(&m_vertex);
if(m_parameters->getRank()==destination) {
cout<<endl;
cout<<"worker: "<<m_workerId<<endl;
cout<<"Receiving RAY_MPI_TAG_REQUEST_VERTEX_READS_REPLY ptr="<<m_pointer<<" from "<<endl;
for(int i=0; i<period; i++)
cout<<" "<<i<<" -> "<<buffer[i];
cout<<endl;
}
#endif
// fancy trick to transmit a void* over the network
unpack_pointer((void**)&m_pointer,buffer[0]);
int rank=buffer[1];
if(rank!=INVALID_RANK) {
#ifdef CONFIG_ASSERT
if(!(rank>=0&&rank<m_parameters->getSize())) {
cout<<"Error rank="<<rank<<endl;
cout<<"Buffer: ";
for(int i=0; i<period; i++) {
cout<<buffer[i]<<" ";
}
cout<<endl;
}
assert(rank>=0&&rank<m_parameters->getSize());
#endif
int readIndex=buffer[2];
int position=buffer[3];
char strand=(char)buffer[4];
#ifdef CONFIG_ASSERT
int destination=m_parameters->vertexRank(&m_vertex);
assert(readIndex>=0);
assert(position>=0);
if(!(strand=='F'||strand=='R')) {
cout<<"Error, invalid strand from "<<destination<<" strand= "<<strand<<" or ";
cout<<buffer[4]<<endl;
}
assert(strand=='F'||strand=='R');
#endif
ReadAnnotation readAnnotation;
readAnnotation.constructor(rank,readIndex,position,strand,false);
m_reads.push_back(readAnnotation);
}
if(m_pointer==NULL) {
m_done=true;
} else {
MessageUnit*message2=(MessageUnit*)m_outboxAllocator->allocate(MAXIMUM_MESSAGE_SIZE_IN_BYTES);
int bufferPosition=0;
m_vertex.pack(message2,&bufferPosition);
MessageUnit integerValue=pack_pointer((void**)&m_pointer);
message2[bufferPosition++]=integerValue;
int period=m_virtualCommunicator->getElementsPerQuery(RAY_MPI_TAG_REQUEST_VERTEX_READS);
// do some padding
while(bufferPosition<period) {
message2[bufferPosition++]=0;
}
int destination=m_parameters->vertexRank(&m_vertex);
Message aMessage(message2,period,destination,RAY_MPI_TAG_REQUEST_VERTEX_READS,m_parameters->getRank());
#ifdef GUILLIMIN_BUG
if(m_parameters->getRank()==destination) {
cout<<endl;
cout<<"worker: "<<m_workerId<<endl;
cout<<"Sending11 RAY_MPI_TAG_REQUEST_VERTEX_READS ptr="<<m_pointer<<" ";
cout<<" integerValue= "<<integerValue<<" to "<<destination<<endl;
for(int i=0; i<period; i++)
cout<<" "<<i<<" -> "<<message2[i];
cout<<endl;
}
#endif
m_virtualCommunicator->pushMessage(m_workerId,&aMessage);
}
}
}
