added cluster.split command

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index f551eddacd00dade4aff87526f0b5aca59ad2b58..f225d50a15670d23f4b3d484901cfb7e30cd2c29 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -144,11 +144,12 @@ int SeqSummaryCommand::execute(){
                                                delete buf2;
                                                
                                                MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
+                                       
+                                               for(int i = 1; i < processors; i++) { 
+                                                       MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+                                                       MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+                                               }
                                                
-                                               //send file positions to all processes
-                                               MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
-                                               MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos        
-                                                               
                                                //figure out how many sequences you have to do
                                                numSeqsPerProcessor = numSeqs / processors;
                                                int startIndex =  pid * numSeqsPerProcessor;
@@ -156,54 +157,55 @@ int SeqSummaryCommand::execute(){
                                                
                                                //do your part
                                                MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
-                                       
-                                               if (m->control_pressed) {  MPI_File_close(&inMPI); MPI_File_close(&outMPI);  return 0;  }
-                                               
-                                               //get the info from the child processes
-                                               for(int i = 1; i < processors; i++) { 
-                                                       
-                                                       int size;
-                                                       MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
-
-                                                       vector<int> temp; temp.resize(size+1);
-                                                       
-                                                       for(int j = 0; j < 5; j++) { 
-                                                       
-                                                               MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status); 
-                                                               int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what count this is for
-                                                               
-                                                               if (receiveTag == startTag) { 
-                                                                       for (int k = 0; k < size; k++) {                startPosition.push_back(temp[k]);       }
-                                                               }else if (receiveTag == endTag) { 
-                                                                       for (int k = 0; k < size; k++) {                endPosition.push_back(temp[k]); }
-                                                               }else if (receiveTag == lengthTag) { 
-                                                                       for (int k = 0; k < size; k++) {                seqLength.push_back(temp[k]);   }
-                                                               }else if (receiveTag == baseTag) { 
-                                                                       for (int k = 0; k < size; k++) {                ambigBases.push_back(temp[k]);  }
-                                                               }else if (receiveTag == lhomoTag) { 
-                                                                       for (int k = 0; k < size; k++) {                longHomoPolymer.push_back(temp[k]);     }
-                                                               }
-                                                       } 
                                                
-                                               }
-
-                                                                                               
                                }else { //i am the child process
                        
-                                       MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+                                       MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPIPos.resize(numSeqs+1);
-                                       MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
-                                       
+                                       MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+                               
                                        //figure out how many sequences you have to align
                                        numSeqsPerProcessor = numSeqs / processors;
                                        int startIndex =  pid * numSeqsPerProcessor;
                                        if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
-                                       
+                               
                                        //do your part
                                        MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
-                                       
-                                       if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); return 0;  }
-                                       
+                               }
+                               
+                               MPI_File_close(&inMPI);
+                               MPI_File_close(&outMPI);
+                               MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+                               
+                               if (pid == 0) {
+                                       //get the info from the child processes
+                                       for(int i = 1; i < processors; i++) { 
+                                               int size;
+                                               MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
+
+                                               vector<int> temp; temp.resize(size+1);
+                                               
+                                               for(int j = 0; j < 5; j++) { 
+                                               
+                                                       MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status); 
+                                                       int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what count this is for
+                                                       
+                                                       if (receiveTag == startTag) { 
+                                                               for (int k = 0; k < size; k++) {                startPosition.push_back(temp[k]);       }
+                                                       }else if (receiveTag == endTag) { 
+                                                               for (int k = 0; k < size; k++) {                endPosition.push_back(temp[k]); }
+                                                       }else if (receiveTag == lengthTag) { 
+                                                               for (int k = 0; k < size; k++) {                seqLength.push_back(temp[k]);   }
+                                                       }else if (receiveTag == baseTag) { 
+                                                               for (int k = 0; k < size; k++) {                ambigBases.push_back(temp[k]);  }
+                                                       }else if (receiveTag == lhomoTag) { 
+                                                               for (int k = 0; k < size; k++) {                longHomoPolymer.push_back(temp[k]);     }
+                                                       }
+                                               } 
+                                       }
+
+                               }else{
+                               
                                        //send my counts
                                        int size = startPosition.size();
                                        MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
@@ -218,12 +220,9 @@ int SeqSummaryCommand::execute(){
                                        ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
                                        longHomoPolymer.push_back(lhomoTag);
                                        ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
-
                                }
                                
-                               MPI_File_close(&inMPI);
-                               MPI_File_close(&outMPI);
-                               
+                               MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                if(processors == 1){
@@ -363,7 +362,10 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {    
        try {
                
+               int pid;
                MPI_Status status; 
+               MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+
                
                for(int i=0;i<num;i++){
                        
@@ -399,7 +401,7 @@ int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPo
                                        
                                MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
                                delete buf3;
-                       }                                               
+                       }       
                }
                
                return 0;