void VerticesExtractor::call_RAY_SLAVE_MODE_ADD_EDGES(){
MACRO_COLLECT_PROFILING_INFORMATION();
if(this->m_outbox==NULL){
m_rank=m_parameters->getRank();
this->m_mode=m_mode;
this->m_outbox=m_outbox;
this->m_outboxAllocator=m_outboxAllocator;
}
if(m_finished){
return;
}
if(!m_checkedCheckpoint){
m_checkedCheckpoint=true;
if(m_parameters->hasCheckpoint("GenomeGraph")){
cout<<"Rank "<<m_parameters->getRank()<<": checkpoint GenomeGraph exists, not extracting vertices."<<endl;
Message aMessage(NULL,0,MASTER_RANK,RAY_MPI_TAG_VERTICES_DISTRIBUTED,m_parameters->getRank());
m_outbox->push_back(aMessage);
m_finished=true;
return;
}
}
#ifdef ASSERT
assert(m_pendingMessages>=0);
#endif
if(m_pendingMessages!=0){
return;
}
if(m_mode_send_vertices_sequence_id%10000==0 &&m_mode_send_vertices_sequence_id_position==0
&&m_mode_send_vertices_sequence_id<(int)m_myReads->size()){
string reverse="";
if(m_reverseComplementVertex==true){
reverse="(reverse complement) ";
}
printf("Rank %i is adding edges %s[%i/%i]\n",m_parameters->getRank(),reverse.c_str(),(int)m_mode_send_vertices_sequence_id+1,(int)m_myReads->size());
fflush(stdout);
m_derivative.addX(m_mode_send_vertices_sequence_id);
m_derivative.printStatus(SLAVE_MODES[RAY_SLAVE_MODE_ADD_EDGES],RAY_SLAVE_MODE_ADD_EDGES);
m_derivative.printEstimatedTime(m_myReads->size());
}
if(m_mode_send_vertices_sequence_id==(int)m_myReads->size()){
MACRO_COLLECT_PROFILING_INFORMATION();
// flush data
flushAll(m_outboxAllocator,m_outbox,m_parameters->getRank());
if(m_pendingMessages==0){
#ifdef ASSERT
assert(m_bufferedDataForIngoingEdges.isEmpty());
assert(m_bufferedDataForOutgoingEdges.isEmpty());
#endif
Message aMessage(NULL,0, MASTER_RANK, RAY_MPI_TAG_VERTICES_DISTRIBUTED,m_parameters->getRank());
m_outbox->push_back(aMessage);
m_finished=true;
printf("Rank %i is adding edges [%i/%i] (completed)\n",m_parameters->getRank(),(int)m_mode_send_vertices_sequence_id,(int)m_myReads->size());
fflush(stdout);
m_bufferedDataForIngoingEdges.showStatistics(m_parameters->getRank());
m_bufferedDataForOutgoingEdges.showStatistics(m_parameters->getRank());
m_derivative.writeFile(&cout);
}
}else{
MACRO_COLLECT_PROFILING_INFORMATION();
/*
* Decode the DNA sequence
* and store it in a local buffer.
*/
if(m_mode_send_vertices_sequence_id_position==0){
(*m_myReads)[(m_mode_send_vertices_sequence_id)]->getSeq(m_readSequence,m_parameters->getColorSpaceMode(),false);
//cout<<"DEBUG Read="<<*m_mode_send_vertices_sequence_id<<" color="<<m_parameters->getColorSpaceMode()<<" Seq= "<<m_readSequence<<endl;
}
int len=strlen(m_readSequence);
if(len<m_parameters->getWordSize()){
m_hasPreviousVertex=false;
(m_mode_send_vertices_sequence_id)++;
(m_mode_send_vertices_sequence_id_position)=0;
return;
}
MACRO_COLLECT_PROFILING_INFORMATION();
char memory[1000];
int maximumPosition=len-m_parameters->getWordSize()+1;
#ifdef ASSERT
assert(m_readSequence!=NULL);
#endif
int p=(m_mode_send_vertices_sequence_id_position);
memcpy(memory,m_readSequence+p,m_parameters->getWordSize());
memory[m_parameters->getWordSize()]='\0';
MACRO_COLLECT_PROFILING_INFORMATION();
if(isValidDNA(memory)){
MACRO_COLLECT_PROFILING_INFORMATION();
Kmer currentForwardKmer=wordId(memory);
/* TODO: possibly don't flush k-mer that are not lower. not sure it that would work though. -Seb */
/*
* previousForwardKmer -> currentForwardKmer
* previousReverseKmer <- currentReverseKmer
*/
/*
* Push the kmer
*/
MACRO_COLLECT_PROFILING_INFORMATION();
if(m_hasPreviousVertex){
MACRO_COLLECT_PROFILING_INFORMATION();
// outgoing edge
// PreviousVertex(*) -> CurrentVertex
Rank outgoingRank=m_parameters->_vertexRank(&m_previousVertex);
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForOutgoingEdges.addAt(outgoingRank,m_previousVertex.getU64(i));
}
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForOutgoingEdges.addAt(outgoingRank,currentForwardKmer.getU64(i));
}
if(m_bufferedDataForOutgoingEdges.flush(outgoingRank,2*KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_OUT_EDGES_DATA,m_outboxAllocator,m_outbox,m_parameters->getRank(),false)){
m_pendingMessages++;
}
// ingoing edge
// PreviousVertex -> CurrentVertex(*)
Rank ingoingRank=m_parameters->_vertexRank(¤tForwardKmer);
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForIngoingEdges.addAt(ingoingRank,m_previousVertex.getU64(i));
}
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForIngoingEdges.addAt(ingoingRank,currentForwardKmer.getU64(i));
}
if(m_bufferedDataForIngoingEdges.flush(ingoingRank,2*KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_IN_EDGES_DATA,m_outboxAllocator,m_outbox,m_parameters->getRank(),false)){
m_pendingMessages++;
}
MACRO_COLLECT_PROFILING_INFORMATION();
}
// reverse complement
//
Kmer currentReverseKmer=currentForwardKmer.
complementVertex(m_parameters->getWordSize(),m_parameters->getColorSpaceMode());
if(m_hasPreviousVertex){
MACRO_COLLECT_PROFILING_INFORMATION();
// outgoing edge
//
Rank outgoingRank=m_parameters->_vertexRank(¤tReverseKmer);
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForOutgoingEdges.addAt(outgoingRank,currentReverseKmer.getU64(i));
}
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForOutgoingEdges.addAt(outgoingRank,m_previousVertexRC.getU64(i));
}
MACRO_COLLECT_PROFILING_INFORMATION();
if(m_bufferedDataForOutgoingEdges.flush(outgoingRank,2*KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_OUT_EDGES_DATA,m_outboxAllocator,m_outbox,m_parameters->getRank(),false)){
m_pendingMessages++;
}
MACRO_COLLECT_PROFILING_INFORMATION();
// ingoing edge
Rank ingoingRank=m_parameters->_vertexRank(&m_previousVertexRC);
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForIngoingEdges.addAt(ingoingRank,currentReverseKmer.getU64(i));
}
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForIngoingEdges.addAt(ingoingRank,m_previousVertexRC.getU64(i));
}
MACRO_COLLECT_PROFILING_INFORMATION();
if(m_bufferedDataForIngoingEdges.flush(ingoingRank,2*KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_IN_EDGES_DATA,m_outboxAllocator,m_outbox,m_parameters->getRank(),false)){
m_pendingMessages++;
}
MACRO_COLLECT_PROFILING_INFORMATION();
}
// there is a previous vertex.
m_hasPreviousVertex=true;
m_previousVertex=currentForwardKmer;
m_previousVertexRC=currentReverseKmer;
}else{
m_hasPreviousVertex=false;
}
MACRO_COLLECT_PROFILING_INFORMATION();
(m_mode_send_vertices_sequence_id_position++);
if((m_mode_send_vertices_sequence_id_position)==maximumPosition){
m_hasPreviousVertex=false;
(m_mode_send_vertices_sequence_id)++;
(m_mode_send_vertices_sequence_id_position)=0;
}
}
MACRO_COLLECT_PROFILING_INFORMATION();
}
void VerticesExtractor::process(int*m_mode_send_vertices_sequence_id,
ArrayOfReads*m_myReads,
bool*m_reverseComplementVertex,
int rank,
StaticVector*m_outbox,
bool*m_mode_send_vertices,
int wordSize,
int size,
RingAllocator*m_outboxAllocator,
int*m_mode
){
if(this->m_outbox==NULL){
m_rank=rank;
this->m_mode=m_mode;
this->m_outbox=m_outbox;
this->m_outboxAllocator=m_outboxAllocator;
}
#ifdef ASSERT
assert(m_pendingMessages>=0);
#endif
if(m_pendingMessages!=0){
return;
}
if(m_finished){
return;
}
if(*m_mode_send_vertices_sequence_id%100000==0 &&m_mode_send_vertices_sequence_id_position==0
&&*m_mode_send_vertices_sequence_id<(int)m_myReads->size()){
string reverse="";
if(*m_reverseComplementVertex==true){
reverse="(reverse complement) ";
}
printf("Rank %i is computing vertices & edges %s[%i/%i]\n",rank,reverse.c_str(),(int)*m_mode_send_vertices_sequence_id+1,(int)m_myReads->size());
fflush(stdout);
}
if(*m_mode_send_vertices_sequence_id>(int)m_myReads->size()-1){
// flush data
flushAll(m_outboxAllocator,m_outbox,rank);
if(m_pendingMessages==0){
#ifdef ASSERT
assert(m_bufferedData.isEmpty());
assert(m_bufferedDataForIngoingEdges.isEmpty());
assert(m_bufferedDataForOutgoingEdges.isEmpty());
#endif
Message aMessage(NULL,0, MASTER_RANK, RAY_MPI_TAG_VERTICES_DISTRIBUTED,rank);
m_outbox->push_back(aMessage);
m_finished=true;
printf("Rank %i is computing vertices & edges [%i/%i] (completed)\n",rank,(int)*m_mode_send_vertices_sequence_id,(int)m_myReads->size());
fflush(stdout);
m_bufferedData.showStatistics(m_parameters->getRank());
m_bufferedDataForIngoingEdges.showStatistics(m_parameters->getRank());
m_bufferedDataForOutgoingEdges.showStatistics(m_parameters->getRank());
}
}else{
if(m_mode_send_vertices_sequence_id_position==0){
(*m_myReads)[(*m_mode_send_vertices_sequence_id)]->getSeq(m_readSequence,m_parameters->getColorSpaceMode(),false);
//cout<<"DEBUG Read="<<*m_mode_send_vertices_sequence_id<<" color="<<m_parameters->getColorSpaceMode()<<" Seq= "<<m_readSequence<<endl;
}
int len=strlen(m_readSequence);
if(len<wordSize){
m_hasPreviousVertex=false;
(*m_mode_send_vertices_sequence_id)++;
(m_mode_send_vertices_sequence_id_position)=0;
return;
}
char memory[1000];
int lll=len-wordSize+1;
#ifdef ASSERT
assert(m_readSequence!=NULL);
#endif
int p=(m_mode_send_vertices_sequence_id_position);
memcpy(memory,m_readSequence+p,wordSize);
memory[wordSize]='\0';
if(isValidDNA(memory)){
Kmer a=wordId(memory);
int rankToFlush=0;
rankToFlush=m_parameters->_vertexRank(&a);
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedData.addAt(rankToFlush,a.getU64(i));
}
if(m_bufferedData.flush(rankToFlush,KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_VERTICES_DATA,m_outboxAllocator,m_outbox,rank,false)){
m_pendingMessages++;
}
if(m_hasPreviousVertex){
// outgoing edge
int outgoingRank=m_parameters->_vertexRank(&m_previousVertex);
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForOutgoingEdges.addAt(outgoingRank,m_previousVertex.getU64(i));
}
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForOutgoingEdges.addAt(outgoingRank,a.getU64(i));
}
if(m_bufferedDataForOutgoingEdges.needsFlushing(outgoingRank,2*KMER_U64_ARRAY_SIZE)){
if(m_bufferedData.flush(outgoingRank,KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_VERTICES_DATA,m_outboxAllocator,m_outbox,rank,true)){
m_pendingMessages++;
}
}
if(m_bufferedDataForOutgoingEdges.flush(outgoingRank,2*KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_OUT_EDGES_DATA,m_outboxAllocator,m_outbox,rank,false)){
m_pendingMessages++;
}
// ingoing edge
int ingoingRank=m_parameters->_vertexRank(&a);
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForIngoingEdges.addAt(ingoingRank,m_previousVertex.getU64(i));
}
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForIngoingEdges.addAt(ingoingRank,a.getU64(i));
}
if(m_bufferedDataForIngoingEdges.needsFlushing(ingoingRank,2*KMER_U64_ARRAY_SIZE)){
if(m_bufferedData.flush(ingoingRank,KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_VERTICES_DATA,m_outboxAllocator,m_outbox,rank,true)){
m_pendingMessages++;
}
}
if(m_bufferedDataForIngoingEdges.flush(ingoingRank,2*KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_IN_EDGES_DATA,m_outboxAllocator,m_outbox,rank,false)){
m_pendingMessages++;
}
}
// reverse complement
Kmer b=complementVertex(&a,wordSize,m_parameters->getColorSpaceMode());
rankToFlush=m_parameters->_vertexRank(&b);
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedData.addAt(rankToFlush,b.getU64(i));
}
if(m_bufferedData.flush(rankToFlush,KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_VERTICES_DATA,m_outboxAllocator,m_outbox,rank,false)){
m_pendingMessages++;
}
if(m_hasPreviousVertex){
// outgoing edge
int outgoingRank=m_parameters->_vertexRank(&b);
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForOutgoingEdges.addAt(outgoingRank,b.getU64(i));
}
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForOutgoingEdges.addAt(outgoingRank,m_previousVertexRC.getU64(i));
}
if(m_bufferedDataForOutgoingEdges.needsFlushing(outgoingRank,2*KMER_U64_ARRAY_SIZE)){
if(m_bufferedData.flush(outgoingRank,1*KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_VERTICES_DATA,m_outboxAllocator,m_outbox,rank,true)){
m_pendingMessages++;
}
}
if(m_bufferedDataForOutgoingEdges.flush(outgoingRank,2*KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_OUT_EDGES_DATA,m_outboxAllocator,m_outbox,rank,false)){
m_pendingMessages++;
}
// ingoing edge
int ingoingRank=m_parameters->_vertexRank(&m_previousVertexRC);
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForIngoingEdges.addAt(ingoingRank,b.getU64(i));
}
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_bufferedDataForIngoingEdges.addAt(ingoingRank,m_previousVertexRC.getU64(i));
}
if(m_bufferedDataForIngoingEdges.needsFlushing(ingoingRank,2*KMER_U64_ARRAY_SIZE)){
if(m_bufferedData.flush(ingoingRank,1*KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_VERTICES_DATA,m_outboxAllocator,m_outbox,rank,true)){
m_pendingMessages++;
}
}
if(m_bufferedDataForIngoingEdges.flush(ingoingRank,2*KMER_U64_ARRAY_SIZE,RAY_MPI_TAG_IN_EDGES_DATA,m_outboxAllocator,m_outbox,rank,false)){
m_pendingMessages++;
}
}
// there is a previous vertex.
m_hasPreviousVertex=true;
m_previousVertex=a;
m_previousVertexRC=b;
}else{
m_hasPreviousVertex=false;
}
(m_mode_send_vertices_sequence_id_position++);
if((m_mode_send_vertices_sequence_id_position)==lll){
m_hasPreviousVertex=false;
(*m_mode_send_vertices_sequence_id)++;
(m_mode_send_vertices_sequence_id_position)=0;
}
}
}