X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;h=66cf12fb8768bcc9c4995256544761e2d8baf820;hb=2a07f8664a7fd1ef0d572b88e8b5bede24cc0b3c;hp=fe919dea41de925a5d27227f3805de3e156f9128;hpb=2bbb7273d4bf5209f098c764551c6e072d60df36;p=mothur.git

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index fe919de..66cf12f 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -167,17 +167,23 @@ int ChimeraCheckCommand::execute(){
 			int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
 			int inMode=MPI_MODE_RDONLY; 
 			
-			char* outFilename = new char[outputFileName.length()];
-			memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
+			//char* outFilename = new char[outputFileName.length()];
+			//memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
+			
+			char outFilename[1024];
+			strcpy(outFilename, outputFileName.c_str());
 
-			char* inFileName = new char[fastafile.length()];
-			memcpy(inFileName, fastafile.c_str(), fastafile.length());
+			//char* inFileName = new char[fastafile.length()];
+			//memcpy(inFileName, fastafile.c_str(), fastafile.length());
+			
+			char inFileName[1024];
+			strcpy(inFileName, fastafile.c_str());
 
 			MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 			MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 			
-			delete outFilename;
-			delete inFileName;
+			//delete outFilename;
+			//delete inFileName;
 
 			if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  delete chimera; return 0;  }
 			
@@ -185,13 +191,16 @@ int ChimeraCheckCommand::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, MPIPos);
@@ -204,14 +213,15 @@ int ChimeraCheckCommand::execute(){
 					MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); 
 				}
 			}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, MPIPos);
@@ -227,6 +237,7 @@ int ChimeraCheckCommand::execute(){
 			//close files 
 			MPI_File_close(&inMPI);
 			MPI_File_close(&outMPI);
+			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 	#else
 		
 		//break up file