X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;h=45f7f545f78d3d239592ccc60c12b2561393e869;hb=9946a1b4b50969d08ce059b248bdeecafbf989ac;hp=0b96f2172359efc9b7ed5ab5c9dcc15e7223dbbc;hpb=a61980e36d61937acccadc41be260165a1e389f4;p=mothur.git

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 0b96f21..45f7f54 100644
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -233,13 +233,16 @@ int ChimeraCcodeCommand::execute(){
 				MPIPos = setFilePosFasta(fastafile, 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(&MPIPos[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(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+				}
 				
 				//figure out how many sequences you have to align
 				numSeqsPerProcessor = numSeqs / processors;
-				if(pid == (processors - 1)){	numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; 	}
 				int startIndex =  pid * numSeqsPerProcessor;
+				if(pid == (processors - 1)){	numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; 	}
+				
 			
 				//align your part
 				driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
@@ -252,14 +255,15 @@ int ChimeraCcodeCommand::execute(){
 					if (tempResult != 0) { MPIWroteAccnos = true; }
 				}
 			}else{ //you are a 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;
-				if(pid == (processors - 1)){	numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; 	}
 				int startIndex =  pid * numSeqsPerProcessor;
+				if(pid == (processors - 1)){	numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; 	}
+				
 				
 				//align your part
 				driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
@@ -274,6 +278,8 @@ int ChimeraCcodeCommand::execute(){
 			MPI_File_close(&outMPI);
 			MPI_File_close(&outMPIAccnos);
 			
+			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+			
 			//delete accnos file if blank
 			if (pid == 0) {
 				if (!MPIWroteAccnos) {