X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=fbf986dc6965de7d9d269c31f35e99ed85467a9d;hb=11c115c802602be50e106aae56969e15d2c49a62;hp=65349352d791f91aceeb850b114b697037984d41;hpb=091640889a47c2fb66b479b3f3262addf3a3fb76;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 6534935..fbf986d 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -31,8 +31,48 @@ Engine::Engine(){
 InteractEngine::InteractEngine(string path){
 
 	globaldata = GlobalData::getInstance();
-	globaldata->argv = path;
 	
+	string temppath = path.substr(0, (path.find_last_of('m')));
+	
+	//this will happen if you set the path variable to contain mothur's exe location
+	if (temppath == "") { 
+	
+		string envPath = getenv("PATH");
+		
+		//delimiting path char
+		char delim;
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			delim = ':';
+		#else
+			delim = ';';
+		#endif
+		
+		//break apart path variable by ':'
+		vector<string> dirs;
+		splitAtChar(envPath, dirs, delim);
+		
+		//get path related to mothur
+		string mothurPath = "";
+		for (int i = 0; i < dirs.size(); i++) {
+			//to lower so we can find it
+			string tempLower = "";
+			for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
+			
+			//is this mothurs path?
+			if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
+		}
+		
+		//add mothur so it looks like what argv would look like
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			mothurPath += "/mothur";
+		#else
+			mothurPath += "\\mothur";
+		#endif
+		
+		path = mothurPath;
+	}
+	
+	globaldata->argv = path;
 }
 
 /***********************************************************************/
@@ -51,6 +91,16 @@ bool InteractEngine::getInput(){
 		
 		while(quitCommandCalled != 1){
 
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				
+				if (pid == 0) {
+				
+			#endif
+			
 			mout->mothurOutEndLine();
 			
 			input = getCommand();	
@@ -60,7 +110,31 @@ bool InteractEngine::getInput(){
 			
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
+
 			
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
+
+			
+			#endif
+		
 			CommandOptionParser parser(input);
 			commandName = parser.getCommandString();
 	
@@ -71,9 +145,9 @@ bool InteractEngine::getInput(){
 					#ifdef USE_MPI
 						int pid;
 						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
- 
-//cout << pid << " is here " << commandName << endl;
+						
 						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					//cout << pid << " is in execute " << commandName << endl;
 					#endif
 					//executes valid command
 					Command* command = cFactory->getCommand(commandName, options);
@@ -99,9 +173,6 @@ bool InteractEngine::getInput(){
 /***********************************************************************/
 string Engine::getCommand()  {
 	try {
-		#ifdef USE_MPI
-			MPI_Barrier(MPI_COMM_WORLD);
-		#endif
 	
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 			#ifdef USE_READLINE
@@ -148,6 +219,47 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 		globaldata = GlobalData::getInstance();
 	
 		openedBatch = openInputFile(batchFileName, inputBatchFile);
+		
+		string temppath = path.substr(0, (path.find_last_of('m')));
+	
+		//this will happen if you set the path variable to contain mothur's exe location
+		if (temppath == "") { 
+		
+			string envPath = getenv("PATH");
+			
+			//delimiting path char
+			char delim;
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				delim = ':';
+			#else
+				delim = ';';
+			#endif
+			
+			//break apart path variable by ':'
+			vector<string> dirs;
+			splitAtChar(envPath, dirs, delim);
+			
+			//get path related to mothur
+			string mothurPath = "";
+			for (int i = 0; i < dirs.size(); i++) {
+				//to lower so we can find it
+				string tempLower = "";
+				for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
+				
+				//is this mothurs path?
+				if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
+			}
+			
+			//add mothur so it looks like what argv would look like
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				mothurPath += "/mothur";
+			#else
+				mothurPath += "\\mothur";
+			#endif
+			
+			path = mothurPath;
+		}
+
 		globaldata->argv = path;
 				
 	}
@@ -180,10 +292,45 @@ bool BatchEngine::getInput(){
 		int quitCommandCalled = 0;
 	    int count = 0;
 		while(quitCommandCalled == 0){
-	
+			
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				
+				if (pid == 0) {
+				
+			#endif
+			
 			input = getNextCommand(inputBatchFile);
 			count++;
 			
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
+
+			
+			#endif
+
+			
+			
 			if (input[0] != '#') {
 				
 				mout->mothurOutEndLine();
@@ -238,11 +385,6 @@ bool BatchEngine::getInput(){
 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 	try {
 		
-		#ifdef USE_MPI
-			int err = MPI_Barrier(MPI_COMM_WORLD);
-//cout << "barrier = " << err << '\t' << MPI_SUCCESS << endl;
-		#endif
-		
 		string nextcommand = "";
 		
 		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
@@ -265,6 +407,46 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 		
 		//remove quotes
 		listOfCommands = commandString.substr(1, (commandString.length()-1));
+		
+		string temppath = path.substr(0, (path.find_last_of('m')));
+	
+		//this will happen if you set the path variable to contain mothur's exe location
+		if (temppath == "") { 
+		
+			string envPath = getenv("PATH");
+			
+			//delimiting path char
+			char delim;
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				delim = ':';
+			#else
+				delim = ';';
+			#endif
+			
+			//break apart path variable by ':'
+			vector<string> dirs;
+			splitAtChar(envPath, dirs, delim);
+			
+			//get path related to mothur
+			string mothurPath = "";
+			for (int i = 0; i < dirs.size(); i++) {
+				//to lower so we can find it
+				string tempLower = "";
+				for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
+				
+				//is this mothurs path?
+				if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
+			}
+			
+			//add mothur so it looks like what argv would look like
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				mothurPath += "/mothur";
+			#else
+				mothurPath += "\\mothur";
+			#endif
+			
+			path = mothurPath;
+		}
 
 		globaldata->argv = path;
 				
@@ -293,7 +475,17 @@ bool ScriptEngine::getInput(){
 		int quitCommandCalled = 0;
 	
 		while(quitCommandCalled == 0){
-		
+			
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				
+				if (pid == 0) {
+				
+			#endif
+			
 			input = getNextCommand(listOfCommands);	
 			
 			if (input == "") { input = "quit()"; }
@@ -302,6 +494,30 @@ bool ScriptEngine::getInput(){
 			mout->mothurOut("mothur > " + input);
 			mout->mothurOutEndLine();
 			
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
+
+			
+			#endif
+			
+			
 			if (mout->control_pressed) { input = "quit()"; }
 				
 			//allow user to omit the () on the quit command
@@ -331,7 +547,7 @@ bool ScriptEngine::getInput(){
 					mout->executing = false;
 									
 					#ifdef USE_MPI
-					cout << pid << " is done in execute" << endl;
+					//cout << pid << " is done in execute" << endl;
 						}
 					#endif
 				}else {		
@@ -353,10 +569,6 @@ bool ScriptEngine::getInput(){
 string ScriptEngine::getNextCommand(string& commandString) {
 	try {
 		
-		#ifdef USE_MPI
-			MPI_Barrier(MPI_COMM_WORLD);
-		#endif
-		
 		string nextcommand = "";
 		int count = 0;