void SeedingData::loadCheckpoint(){
cout<<"Rank "<<m_parameters->getRank()<<" is reading checkpoint Seeds"<<endl;
ifstream f(m_parameters->getCheckpointFile("Seeds").c_str());
int n=0;
f.read((char*)&n,sizeof(int));
for(int i=0;i<n;i++){
GraphPath seed;
seed.setKmerLength(m_parameters->getWordSize());
int vertices=0;
f.read((char*)&vertices,sizeof(int));
for(int j=0;j<vertices;j++){
Kmer kmer;
kmer.read(&f);
seed.push_back(&kmer);
CoverageDepth coverageValue=0;
f.read((char*)&coverageValue,sizeof(CoverageDepth));
seed.addCoverageValue(coverageValue);
}
seed.computePeakCoverage();
m_SEEDING_seeds.push_back(seed);
}
cout<<"Rank "<<m_parameters->getRank()<<" loaded "<<n<<" seeds from checkpoint Seeds"<<endl;
f.close();
}
void SeedingData::loadCheckpoint(){
cout<<"Rank "<<m_parameters->getRank()<<" is reading checkpoint Seeds"<<endl;
ifstream f(m_parameters->getCheckpointFile("Seeds").c_str());
int n=0;
f.read((char*)&n,sizeof(int));
for(int i=0;i<n;i++){
vector<Kmer> seed;
int vertices=0;
f.read((char*)&vertices,sizeof(int));
for(int j=0;j<vertices;j++){
Kmer kmer;
kmer.read(&f);
seed.push_back(kmer);
}
m_SEEDING_seeds.push_back(seed);
}
cout<<"Rank "<<m_parameters->getRank()<<" loaded "<<n<<" seeds from checkpoint Seeds"<<endl;
f.close();
}
void FusionData::distribute(SeedingData*m_seedingData,ExtensionData*m_ed,int getRank,RingAllocator*m_outboxAllocator,StaticVector*m_outbox,int getSize1,int*m_mode){
/** read the checkpoint ContigPaths */
if(!m_processedCheckpoint){
m_processedCheckpoint=true;
if(m_parameters->hasCheckpoint("ContigPaths")){
cout<<"Rank "<<m_parameters->getRank()<<" is reading checkpoint ContigPaths"<<endl;
ifstream f(m_parameters->getCheckpointFile("ContigPaths").c_str());
/* delete old stuff */
m_ed->m_EXTENSION_identifiers.clear();
m_ed->m_EXTENSION_contigs.clear();
int theSize=0;
f.read((char*)&theSize,sizeof(int));
/* write each path with its name and vertices */
for(int i=0;i<theSize;i++){
uint64_t name=0;
int vertices=0;
f.read((char*)&name,sizeof(uint64_t));
f.read((char*)&vertices,sizeof(int));
vector<Kmer> path;
for(int j=0;j<vertices;j++){
Kmer kmer;
kmer.read(&f);
path.push_back(kmer);
}
#ifdef ASSERT
assert(vertices!=0);
assert(vertices == (int)path.size());
#endif
m_ed->m_EXTENSION_identifiers.push_back(name);
m_ed->m_EXTENSION_contigs.push_back(path);
}
f.close();
}
}
if(!isReady()){
return;
}
if(!m_buffers.isEmpty() && m_seedingData->m_SEEDING_i==(uint64_t)m_ed->m_EXTENSION_contigs.size()){
m_ready+=m_buffers.flushAll(RAY_MPI_TAG_SAVE_WAVE_PROGRESSION_WITH_REPLY,m_outboxAllocator,m_outbox,getRank);
return;
}else if(m_buffers.isEmpty() && m_seedingData->m_SEEDING_i==(uint64_t)m_ed->m_EXTENSION_contigs.size()){
printf("Rank %i is distributing fusions [%i/%i] (completed)\n",getRank,(int)m_ed->m_EXTENSION_contigs.size(),(int)m_ed->m_EXTENSION_contigs.size());
fflush(stdout);
Message aMessage(NULL,0,MASTER_RANK,RAY_MPI_TAG_DISTRIBUTE_FUSIONS_FINISHED,getRank);
m_outbox->push_back(aMessage);
(*m_mode)=RAY_SLAVE_MODE_DO_NOTHING;
m_buffers.showStatistics(m_parameters->getRank());
m_buffers.clear();
m_cacheForRepeatedVertices.clear();
m_cacheAllocator.clear();
if(m_parameters->showMemoryUsage()){
showMemoryUsage(m_rank);
showDate();
}
return;
}
if(m_ed->m_EXTENSION_currentPosition==0){
if(m_seedingData->m_SEEDING_i%10==0){
printf("Rank %i is distributing fusions [%i/%i]\n",getRank,(int)(m_seedingData->m_SEEDING_i+1),(int)m_ed->m_EXTENSION_contigs.size());
fflush(stdout);
if(m_parameters->showMemoryUsage()){
showMemoryUsage(getRank);
showDate();
}
}
}
#ifdef ASSERT
assert(m_seedingData->m_SEEDING_i<m_ed->m_EXTENSION_contigs.size());
assert(m_ed->m_EXTENSION_currentPosition < (int) m_ed->m_EXTENSION_contigs[m_seedingData->m_SEEDING_i].size());
assert(m_ed->m_EXTENSION_contigs[m_seedingData->m_SEEDING_i].size() > 0);
#endif
Kmer vertex=m_ed->m_EXTENSION_contigs[m_seedingData->m_SEEDING_i][m_ed->m_EXTENSION_currentPosition];
int destination=m_parameters->_vertexRank(&vertex);
for(int i=0;i<KMER_U64_ARRAY_SIZE;i++){
m_buffers.addAt(destination,vertex.getU64(i));
}
m_buffers.addAt(destination,m_ed->m_EXTENSION_identifiers[m_seedingData->m_SEEDING_i]);
m_buffers.addAt(destination,m_ed->m_EXTENSION_currentPosition);
if(m_buffers.flush(destination,KMER_U64_ARRAY_SIZE+2,RAY_MPI_TAG_SAVE_WAVE_PROGRESSION_WITH_REPLY,m_outboxAllocator,m_outbox,getRank,false)){
m_ready++;
}
m_ed->m_EXTENSION_currentPosition++;
// the next one
if(m_ed->m_EXTENSION_currentPosition==(int)m_ed->m_EXTENSION_contigs[m_seedingData->m_SEEDING_i].size()){
m_seedingData->m_SEEDING_i++;
m_ed->m_EXTENSION_currentPosition=0;
}
}
