X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bellerophon.cpp;h=f4d04ea074b1d2d95cb9bcff4fcc3084e7f234c6;hb=fca3f55d5ded10c3dc77856f3cc4a1c53b02bb6f;hp=54025eb9285c87be35039a3051454cfd763a3c4d;hpb=6f4b9401f7deb8aaf0d87659298308f4138cc3b0;p=mothur.git

diff --git a/bellerophon.cpp b/bellerophon.cpp
index 54025eb..f4d04ea 100644
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -75,7 +75,7 @@ Bellerophon::Bellerophon(string name, bool filterSeqs,  bool c, int win, int inc
 }
 
 //***************************************************************************************************************
-int Bellerophon::print(ostream& out, ostream& outAcc) {
+int Bellerophon::print(ostream& out, ostream& outAcc, string s) {
 	try {
 		int above1 = 0;
 		
@@ -130,7 +130,7 @@ int Bellerophon::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-int Bellerophon::print(MPI_File& out, MPI_File& outAcc) {
+int Bellerophon::print(MPI_File& out, MPI_File& outAcc, string s) {
 	try {
 	
 		int pid;
@@ -246,7 +246,7 @@ int Bellerophon::getChimeras() {
 		numSeqsPerProcessor = iters / processors;
 		
 		//each process hits this only once
-		int startPos = pid * numSeqsPerProcessor;
+		unsigned long int startPos = pid * numSeqsPerProcessor;
 		if(pid == processors - 1){
 				numSeqsPerProcessor = iters - pid * numSeqsPerProcessor;
 		}
@@ -310,7 +310,7 @@ int Bellerophon::getChimeras() {
 			
 			MPIBestSend.clear();
 		}
-		
+		MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 	#else
 	
 		//divide breakpoints between processors
@@ -326,7 +326,7 @@ int Bellerophon::getChimeras() {
 				int numSeqsPerProcessor = iters / processors;
 				
 				for (int i = 0; i < processors; i++) {
-					int startPos = i * numSeqsPerProcessor;
+					unsigned long int startPos = i * numSeqsPerProcessor;
 					if(i == processors - 1){
 						numSeqsPerProcessor = iters - i * numSeqsPerProcessor;
 					}
@@ -373,7 +373,11 @@ int Bellerophon::createProcesses(vector<int> mid) {
 				string tempOut = outputDir + toString(getpid()) + ".temp";
 				writePrefs(tempOut, lines[process]);
 				exit(0);
-			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+			}else { 
+				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+				exit(0);
+			}
 		}
 		
 		//force parent to wait until all the processes are done
@@ -531,7 +535,6 @@ int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* spar
 int Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
 	try {
 		
-		float dme = 0.0;
 		SeqMap::iterator itR;
 		SeqMap::iterator itL;
 		
@@ -665,7 +668,7 @@ int Bellerophon::writePrefs(string file, linePair tempLine) {
 	try {
 	
 		ofstream outTemp;
-		openOutputFile(file, outTemp);
+		m->openOutputFile(file, outTemp);
 		
 		//lets you know what part of the pref matrix you are writing
 		outTemp << tempLine.start << '\t' << tempLine.num << endl;
@@ -695,12 +698,12 @@ int Bellerophon::readPrefs(string file) {
 	try {
 	
 		ifstream inTemp;
-		openInputFile(file, inTemp);
+		m->openInputFile(file, inTemp);
 		
 		int start, num;
 		
 		//lets you know what part of the pref matrix you are writing
-		inTemp >> start >> num;  gobble(inTemp);
+		inTemp >> start >> num;  m->gobble(inTemp);
 		
 		for (int i = start; i < num; i++) {
 			
@@ -710,7 +713,7 @@ int Bellerophon::readPrefs(string file) {
 			
 				inTemp >> pref[i][j].name >> pref[i][j].leftParent >> pref[i][j].rightParent;
 				inTemp >> pref[i][j].score >> pref[i][j].closestLeft >> pref[i][j].closestRight >> pref[i][j].midpoint;
-				gobble(inTemp);
+				m->gobble(inTemp);
 			}
 		}