changed the daughterLevels in classifiers summary file to reflect the classifications...

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 85883282ed841c4f22bba3dda6e39e83fe5287c7..7d015a85aed7e084926a918888f6e5ee761228cc 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -419,8 +419,10 @@ int ClassifySeqsCommand::execute(){
                                        MPIPos = setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
                                        
                                        //send file positions to all processes
-                                       MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
-                                       MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos   
+                                       for(int i = 1; i < processors; i++) { 
+                                               MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+                                               MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+                                       }
                                        
                                        //figure out how many sequences you have to align
                                        numSeqsPerProcessor = numFastaSeqs / processors;
@@ -438,9 +440,9 @@ int ClassifySeqsCommand::execute(){
                                                MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
                                        }
                                }else{ //you are a child process
-                                       MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+                                       MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPIPos.resize(numFastaSeqs+1);
-                                       MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+                                       MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
                                        
                                        //figure out how many sequences you have to align
                                        numSeqsPerProcessor = numFastaSeqs / processors;
@@ -461,6 +463,7 @@ int ClassifySeqsCommand::execute(){
                                MPI_File_close(&inMPI);
                                MPI_File_close(&outMPINewTax);
                                MPI_File_close(&outMPITempTax);
+                               MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                                
 #else
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -526,6 +529,11 @@ int ClassifySeqsCommand::execute(){
        #endif  
 #endif
 
+               m->mothurOutEndLine();
+               m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+               start = time(NULL);
+
+
                #ifdef USE_MPI  
                        if (pid == 0) {  //this part does not need to be paralellized
                        
@@ -556,10 +564,6 @@ int ClassifySeqsCommand::execute(){
                        }
                #endif
 
-                       m->mothurOutEndLine();
-                       m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
-                       start = time(NULL);
-                       
                        string group = "";
                        if (groupfile != "") {  group = groupfileNames[s]; }
                        
@@ -631,7 +635,7 @@ int ClassifySeqsCommand::execute(){
                        rename(unclass.c_str(), newTaxonomyFile.c_str());
                        
                        m->mothurOutEndLine();
-                       m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for  " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+                       m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
                        
                        #ifdef USE_MPI  
                                }