diff --git a/code/MessageProcessor/MessageProcessor.cpp b/code/MessageProcessor/MessageProcessor.cpp index 0a48f8e..da74e9c 100644 --- a/code/MessageProcessor/MessageProcessor.cpp +++ b/code/MessageProcessor/MessageProcessor.cpp @@ -413,9 +413,10 @@ void MessageProcessor::call_RAY_MPI_TAG_REQUEST_VERTEX_READS(Message*message){ } void MessageProcessor::call_RAY_MPI_TAG_SET_WORD_SIZE(Message*message){ + /* void*buffer=message->getBuffer(); MessageUnit*incoming=(MessageUnit*)buffer; - (*m_wordSize)=incoming[0]; + */ } /* @@ -812,7 +813,7 @@ void MessageProcessor::call_RAY_MPI_TAG_PURGE_NULL_EDGES(Message*message){ #ifdef ASSERT GridTableIterator iterator; - iterator.constructor(m_subgraph,*m_wordSize,m_parameters); + iterator.constructor(m_subgraph, m_parameters->getWordSize(),m_parameters); LargeCount n=0; @@ -875,7 +876,7 @@ void MessageProcessor::call_RAY_MPI_TAG_OUT_EDGES_DATA(Message*message){ continue; /* NULL because coverage is too low */ } - node->addOutgoingEdge(&prefix,&suffix,(*m_wordSize)); + node->addOutgoingEdge(&prefix,&suffix, m_parameters->getWordSize()); } Message aMessage(NULL,0,message->getSource(),RAY_MPI_TAG_OUT_EDGES_DATA_REPLY,m_rank); @@ -934,7 +935,7 @@ void MessageProcessor::call_RAY_MPI_TAG_IN_EDGES_DATA(Message*message){ continue; } - node->addIngoingEdge(&suffix,&prefix,(*m_wordSize)); + node->addIngoingEdge(&suffix,&prefix, m_parameters->getWordSize()); /* * Make sure that the edge was added. @@ -1279,7 +1280,7 @@ void MessageProcessor::call_RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES(Message*me Vertex*node=m_subgraph->find(&vertex); vector outgoingEdges; if(node!=NULL) - outgoingEdges=node->getOutgoingEdges(&vertex,*m_wordSize); + outgoingEdges=node->getOutgoingEdges(&vertex, m_parameters->getWordSize()); int outputPosition=(1+4*KMER_U64_ARRAY_SIZE)*i; message2[outputPosition++]=outgoingEdges.size(); for(int j=0;j<(int)outgoingEdges.size();j++){ @@ -1307,8 +1308,8 @@ void MessageProcessor::call_RAY_MPI_TAG_REQUEST_VERTEX_EDGES(Message*message){ assert(node!=NULL); #endif - vector outgoingEdges=node->getOutgoingEdges(&vertex,*m_wordSize); - vector ingoingEdges=node->getIngoingEdges(&vertex,*m_wordSize); + vector outgoingEdges=node->getOutgoingEdges(&vertex, m_parameters->getWordSize()); + vector ingoingEdges=node->getIngoingEdges(&vertex, m_parameters->getWordSize()); message2[outputPosition++]=outgoingEdges.size(); for(int i=0;i<(int)outgoingEdges.size();i++){ @@ -1444,11 +1445,13 @@ void MessageProcessor::call_RAY_MPI_TAG_REQUEST_VERTEX_INGOING_EDGES(Message*mes Vertex*node=m_subgraph->find(&vertex); #ifdef ASSERT if(node==NULL){ - cout<<"Rank="<getColorSpaceMode())<<" does not exist."<getWordSize(), + m_parameters->getColorSpaceMode())<<" does not exist."< ingoingEdges=node->getIngoingEdges(&vertex,*m_wordSize); + vector ingoingEdges=node->getIngoingEdges(&vertex, + m_parameters->getWordSize()); int outputPosition=i*5; message2[outputPosition++]=ingoingEdges.size(); for(int j=0;j<(int)ingoingEdges.size();j++){ @@ -1564,7 +1567,8 @@ void MessageProcessor::call_RAY_MPI_TAG_ASK_READ_VERTEX_AT_POSITION(Message*mess Rank source=message->getSource(); MessageUnit*incoming=(MessageUnit*)buffer; Strand strand=incoming[2]; - Kmer vertex=(*m_myReads)[incoming[0]]->getVertex(incoming[1],(*m_wordSize),strand,m_parameters->getColorSpaceMode()); + Kmer vertex=(*m_myReads)[incoming[0]]->getVertex(incoming[1], m_parameters->getWordSize(), + strand,m_parameters->getColorSpaceMode()); MessageUnit*message2=(MessageUnit*)m_outboxAllocator->allocate(1*sizeof(MessageUnit)); int bufferPosition=0; vertex.pack(message2,&bufferPosition); @@ -1744,7 +1748,8 @@ void MessageProcessor::call_RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE(Message*message){ #ifdef ASSERT Vertex*node=m_subgraph->find(&vertex); if(node==NULL){ - cout<<"Source="<getSource()<<" Destination="<getColorSpaceMode())<<" does not exist, aborting"<getWordSize(), + m_parameters->getColorSpaceMode())<<" does not exist, aborting"<getWordSize(), m_parameters); #ifdef ASSERT LargeCount cleared=0; @@ -2164,7 +2169,7 @@ void MessageProcessor::call_RAY_MPI_TAG_CLEAR_DIRECTIONS(Message*message){ Kmer otherKmer; m_ed->m_EXTENSION_contigs[i].at(j,&otherKmer); - Kmer kmer=otherKmer.complementVertex(*m_wordSize, + Kmer kmer=otherKmer.complementVertex(m_parameters->getWordSize(), m_parameters->getColorSpaceMode()); rc.push_back(&kmer); } @@ -2485,7 +2490,6 @@ SequencesLoader*sequencesLoader,ExtensionData*ed, int rank, int*m_numberOfMachinesDoneSendingEdges, FusionData*m_fusionData, - int*m_wordSize, ArrayOfReads*m_myReads, int size, RingAllocator*m_inboxAllocator, @@ -2536,7 +2540,6 @@ SequencesIndexer*m_si){ m_rank=rank; this->m_numberOfMachinesDoneSendingEdges=m_numberOfMachinesDoneSendingEdges; this->m_fusionData=m_fusionData; - this->m_wordSize=m_wordSize; this->m_myReads=m_myReads; m_size=size; this->m_inboxAllocator=m_inboxAllocator; diff --git a/code/MessageProcessor/MessageProcessor.h b/code/MessageProcessor/MessageProcessor.h index 91a9285..e64165c 100644 --- a/code/MessageProcessor/MessageProcessor.h +++ b/code/MessageProcessor/MessageProcessor.h @@ -474,7 +474,6 @@ class MessageProcessor : public CorePlugin { int m_rank; int*m_numberOfMachinesDoneSendingEdges; FusionData*m_fusionData; - int*m_wordSize; ArrayOfReads*m_myReads; int m_size; SequencesIndexer*m_si; @@ -531,7 +530,6 @@ ExtensionData*ed, int rank, int*m_numberOfMachinesDoneSendingEdges, FusionData*m_fusionData, - int*m_wordSize, ArrayOfReads*m_myReads, int size, RingAllocator*m_inboxAllocator, diff --git a/code/SeedingData/SeedingData.cpp b/code/SeedingData/SeedingData.cpp index 11968e6..884f8cc 100644 --- a/code/SeedingData/SeedingData.cpp +++ b/code/SeedingData/SeedingData.cpp @@ -313,7 +313,7 @@ RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE void SeedingData::constructor(SeedExtender*seedExtender,int rank,int size,StaticVector*outbox,RingAllocator*outboxAllocator, int*mode, - Parameters*parameters,int*wordSize,GridTable*subgraph,StaticVector*inbox, + Parameters*parameters,GridTable*subgraph,StaticVector*inbox, VirtualCommunicator*vc){ m_skippedObjectsWithDeadEndForHead=0; diff --git a/code/SeedingData/SeedingData.h b/code/SeedingData/SeedingData.h index dcc6592..c120c4a 100644 --- a/code/SeedingData/SeedingData.h +++ b/code/SeedingData/SeedingData.h @@ -172,7 +172,7 @@ public: void call_RAY_SLAVE_MODE_START_SEEDING(); void constructor(SeedExtender*seedExtender,int rank,int size,StaticVector*outbox,RingAllocator*outboxAllocator, - int*mode,Parameters*parameters,int*wordSize,GridTable*subgraph, + int*mode,Parameters*parameters,GridTable*subgraph, StaticVector*inbox,VirtualCommunicator*vc); void updateStates(); diff --git a/code/application_core/Machine.cpp b/code/application_core/Machine.cpp index d31167b..2f19d5e 100644 --- a/code/application_core/Machine.cpp +++ b/code/application_core/Machine.cpp @@ -190,7 +190,6 @@ void Machine::start(){ m_numberOfMachinesReadyForEdgesDistribution=0; m_aborted=false; m_readyToSeed=0; - m_wordSize=-1; m_last_value=0; m_mode_send_ingoing_edges=false; m_mode_send_vertices=false; @@ -479,7 +478,7 @@ void Machine::start(){ if(!oldDirectoryExists) m_subgraph.printStatus(); - m_seedingData->constructor(&m_seedExtender,getRank(),getSize(),m_outbox,m_outboxAllocator,m_switchMan->getSlaveModePointer(),&m_parameters,&m_wordSize,&m_subgraph,m_inbox,m_virtualCommunicator); + m_seedingData->constructor(&m_seedExtender,getRank(),getSize(),m_outbox,m_outboxAllocator,m_switchMan->getSlaveModePointer(),&m_parameters,&m_subgraph,m_inbox,m_virtualCommunicator); (*m_alive)=true; m_totalLetters=0; @@ -502,7 +501,6 @@ m_seedingData, getRank(), &m_numberOfMachinesDoneSendingEdges, m_fusionData, - &m_wordSize, &m_myReads, getSize(), m_inboxAllocator, diff --git a/code/application_core/Machine.h b/code/application_core/Machine.h index 1ae8c33..99aa34b 100644 --- a/code/application_core/Machine.h +++ b/code/application_core/Machine.h @@ -179,7 +179,6 @@ class Machine : public MiniRank{ MessageProcessor m_mp; int m_argc; char**m_argv; - int m_wordSize; int m_last_value; time_t m_lastTime; bool m_mode_send_outgoing_edges;