fixes while testing

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index f67dba7223eded3e55cc104841657ee229bc0db8..66e0cb07e066c27724480f1f1c6c523ff755e8d6 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -217,8 +217,10 @@ int ScreenSeqsCommand::execute(){
                                MPIPos = setFilePosFasta(fastafile, 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;
@@ -249,10 +251,10 @@ int ScreenSeqsCommand::execute(){
                                        }*/
                                }
                        }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;
                                int startIndex =  pid * numSeqsPerProcessor;
@@ -285,6 +287,7 @@ int ScreenSeqsCommand::execute(){
                        MPI_File_close(&outMPIGood);
                        MPI_File_close(&outMPIBad);
                        MPI_File_close(&outMPIBadAccnos);
+                       MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                                        
 #else
                                        
@@ -292,7 +295,7 @@ int ScreenSeqsCommand::execute(){
                        if(processors == 1){
                                ifstream inFASTA;
                                openInputFile(fastafile, inFASTA);
-                               numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               getNumSeqs(inFASTA, numFastaSeqs);
                                inFASTA.close();
                                
                                lines.push_back(new linePair(0, numFastaSeqs));
@@ -366,7 +369,7 @@ int ScreenSeqsCommand::execute(){
        #else
                        ifstream inFASTA;
                        openInputFile(fastafile, inFASTA);
-                       numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                       getNumSeqs(inFASTA, numFastaSeqs);
                        inFASTA.close();
                        
                        lines.push_back(new linePair(0, numFastaSeqs));