X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=bellerophon.cpp;h=833cfb907d6d4bd2aed8acb3d8522932ac3b2e7d;hp=54025eb9285c87be35039a3051454cfd763a3c4d;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=6f4b9401f7deb8aaf0d87659298308f4138cc3b0

diff --git a/bellerophon.cpp b/bellerophon.cpp
index 54025eb..833cfb9 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 long startPos = pid * numSeqsPerProcessor;
 		if(pid == processors - 1){
 				numSeqsPerProcessor = iters - pid * numSeqsPerProcessor;
 		}
@@ -274,7 +274,7 @@ int Bellerophon::getChimeras() {
 					MPI_Recv(&length, 1, MPI_INT, j, 2001, MPI_COMM_WORLD, &status);
 					
 					char* buf = new char[length];
-					MPI_Recv(&buf, length, MPI_CHAR, j, 2001, MPI_COMM_WORLD, &status);
+					MPI_Recv(&buf[0], length, MPI_CHAR, j, 2001, MPI_COMM_WORLD, &status);
 					
 					string temp = buf;
 					if (temp.length() > length) { temp = temp.substr(0, length); }
@@ -293,7 +293,7 @@ int Bellerophon::getChimeras() {
 			//played with this a bit, but it may be better to try user-defined datatypes with set string lengths??
 			vector<string> MPIBestSend = getBestWindow(lines[0]);
 			pref.clear();
-			
+				
 			//send your result to parent
 			for (int i = 0; i < numSeqs; i++) {
 				
@@ -310,11 +310,11 @@ int Bellerophon::getChimeras() {
 			
 			MPIBestSend.clear();
 		}
-		
+		MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 	#else
 	
 		//divide breakpoints between processors
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			if(processors == 1){ 
 				lines.push_back(linePair(0, iters));	
 				
@@ -326,7 +326,7 @@ int Bellerophon::getChimeras() {
 				int numSeqsPerProcessor = iters / processors;
 				
 				for (int i = 0; i < processors; i++) {
-					int startPos = i * numSeqsPerProcessor;
+					unsigned long long startPos = i * numSeqsPerProcessor;
 					if(i == processors - 1){
 						numSeqsPerProcessor = iters - i * numSeqsPerProcessor;
 					}
@@ -356,7 +356,7 @@ int Bellerophon::getChimeras() {
 
 int Bellerophon::createProcesses(vector<int> mid) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 0;
 		int exitCommand = 1;
 		vector<int> processIDS;
@@ -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;
@@ -674,7 +677,7 @@ int Bellerophon::writePrefs(string file, linePair tempLine) {
 			
 			for (int j = 0; j < numSeqs; j++) {
 				
-				if (m->control_pressed) { outTemp.close(); remove(file.c_str()); return 0; }
+				if (m->control_pressed) { outTemp.close(); m->mothurRemove(file); return 0; }
 				
 				outTemp << pref[i][j].name << '\t' << pref[i][j].leftParent << '\t' << pref[i][j].rightParent << '\t';
 				outTemp << pref[i][j].score << '\t' << pref[i][j].closestLeft << '\t' << pref[i][j].closestRight << '\t' << pref[i][j].midpoint <<  endl;
@@ -695,28 +698,28 @@ 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++) {
 			
 			for (int j = 0; j < numSeqs; j++) {
 				
-				if (m->control_pressed) { inTemp.close(); remove(file.c_str()); return 0; }
+				if (m->control_pressed) { inTemp.close(); m->mothurRemove(file); return 0; }
 			
 				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);
 			}
 		}
 		
 		inTemp.close();
 		
-		remove(file.c_str());
+		m->mothurRemove(file);
 		
 		return 0;
 	}