X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignmentdb.cpp;h=bf46bec168858853a58730fd80b4309798982fa6;hb=956cdff34f2d609a7736838b1631cd7957580b8b;hp=364ef12588223c0300eccd767aac6f17e6630aa1;hpb=4a2d841cb97fb02351022efe9d7068b1dc212bf9;p=mothur.git

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 364ef12..bf46bec 100644
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -25,12 +25,14 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 		m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t");	cout.flush();
 		
 		#ifdef USE_MPI	
-			int pid;
-			vector<long> positions;
+			int pid, processors;
+			vector<unsigned long int> positions;
 		
 			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);
+			int tag = 2001;
 	
 			char inFileName[1024];
 			strcpy(inFileName, fastaFileName.c_str());
@@ -41,12 +43,14 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 				positions = setFilePosFasta(fastaFileName, 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
+				MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 				positions.resize(numSeqs+1);
-				MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+				MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 			}
 		
 			//read file 
@@ -73,7 +77,9 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 					if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length()+1; }
 				}
 			}
-		
+			
+			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+			
 			MPI_File_close(&inMPI);
 		
 	#else