added cluster.split command

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 147f499b87357f5782b98fc882db80f3233f2aee..e07344d4678a0ca263008e4b10d4d125ad8ef122 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -27,12 +27,14 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                
                m->mothurOut("Generating search database...    "); cout.flush();
 #ifdef USE_MPI 
-                       int pid;
+                       int pid, processors;
                        vector<long> positions;
+                       int tag = 2001;
                
                        MPI_Status status; 
                        MPI_File inMPI;
                        MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+                       MPI_Comm_size(MPI_COMM_WORLD, &processors);
 
                        //char* inFileName = new char[tempFile.length()];
                        //memcpy(inFileName, tempFile.c_str(), tempFile.length());
@@ -47,12 +49,14 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                positions = setFilePosFasta(tempFile, numSeqs); //fills MPIPos, returns numSeqs
 
                                //send file positions to all processes
-                               MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
-                               MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos     
+                               for(int i = 1; i < processors; i++) { 
+                                       MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+                                       MPI_Send(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+                               }
                        }else{
-                               MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
-                               positions.resize(numSeqs);
-                               MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+                               MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+                               positions.resize(numSeqs+1);
+                               MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
                        }
                        
                        //create database
@@ -86,6 +90,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                        
                        database->generateDB();
                        MPI_File_close(&inMPI);
+                       MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
        #else
                
                //need to know number of template seqs for suffixdb
@@ -171,12 +176,14 @@ int Classify::readTaxonomy(string file) {
                m->mothurOut("Reading in the " + file + " taxonomy...\t");      cout.flush();
 
 #ifdef USE_MPI 
-               int pid, num;
+               int pid, num, processors;
                vector<long> positions;
+               int tag = 2001;
                
                MPI_Status status; 
                MPI_File inMPI;
                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+               MPI_Comm_size(MPI_COMM_WORLD, &processors);
 
                //char* inFileName = new char[file.length()];
                //memcpy(inFileName, file.c_str(), file.length());
@@ -191,12 +198,14 @@ int Classify::readTaxonomy(string file) {
                        positions = setFilePosEachLine(file, num);
                        
                        //send file positions to all processes
-                       MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
-                       MPI_Bcast(&positions[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos 
+                       for(int i = 1; i < processors; i++) { 
+                               MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+                               MPI_Send(&positions[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+                       }
                }else{
-                       MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
-                       positions.resize(num);
-                       MPI_Bcast(&positions[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+                       MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+                       positions.resize(num+1);
+                       MPI_Recv(&positions[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
                }
        
                //read file 
@@ -218,6 +227,7 @@ int Classify::readTaxonomy(string file) {
                }
                
                MPI_File_close(&inMPI);
+               MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else                          
                ifstream inTax;
                openInputFile(file, inTax);