X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=7bacec5c0e757c7b77d3c8801970c17bd3cc5a4a;hb=9013e13ecfb2fda3c2664a76f76cc99b8c7fa74c;hp=acd417cd8477516f2a670f6a34257964d6c442c3;hpb=1f78a8c454a636f19b4711bd52782ea1e3e81d3d;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index acd417c..7bacec5 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -51,6 +51,16 @@ 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 +70,31 @@ 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();
 	
@@ -72,14 +106,8 @@ bool InteractEngine::getInput(){
 						int pid;
 						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
 						
-						if ((pid != 0) && !(cFactory->MPIEnabled(commandName))) {
-cout << pid << " is waiting " << commandName << endl;						
-							char buf[4];
-							MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
-						}
- 
-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);
@@ -88,13 +116,6 @@ cout << pid << " is here " << commandName << endl;
 					mout->executing = false;
 										
 					#ifdef USE_MPI
-							if (!(cFactory->MPIEnabled(commandName))) {
-								char buf[4];
-								strcpy(buf, "done"); 
-
-								MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
-				cout << pid << " is broadcasting " << endl;
-							}
 						}
 					#endif
 				}else {		
@@ -112,6 +133,7 @@ cout << pid << " is here " << commandName << endl;
 /***********************************************************************/
 string Engine::getCommand()  {
 	try {
+	
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 			#ifdef USE_READLINE
 				char* nextCommand = NULL;
@@ -187,11 +209,46 @@ bool BatchEngine::getInput(){
 		
 		//CommandFactory cFactory;
 		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);
 	
-			if (inputBatchFile.eof()) { input = "quit()"; }
-			else { input = getline(inputBatchFile); }
+					}
+				}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] != '#') {
 				
@@ -214,13 +271,7 @@ bool BatchEngine::getInput(){
 						int pid;
 						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
 						
-						if ((pid != 0) && !(cFactory->MPIEnabled(commandName))) {
-cout << pid << " is waiting " << commandName << endl;						
-							char buf[4];
-							MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
-						}
- 
-cout << pid << " is here " << commandName << endl;
+//cout << pid << " is here " << commandName << '\t' << count << endl;
 						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 					#endif
 					//executes valid command
@@ -230,13 +281,6 @@ cout << pid << " is here " << commandName << endl;
 					mout->executing = false;
 										
 					#ifdef USE_MPI
-							if (!(cFactory->MPIEnabled(commandName))) {
-								char buf[4];
-								strcpy(buf, "done"); 
-
-								MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
-				cout << pid << " is broadcasting " << endl;
-							}
 						}
 					#endif
 				}else {		
@@ -256,7 +300,22 @@ cout << pid << " is here " << commandName << endl;
 		exit(1);
 	}
 }
-
+/***********************************************************************/
+string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
+	try {
+		
+		string nextcommand = "";
+		
+		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
+		else { nextcommand = getline(inputBatchFile); }
+		
+		return nextcommand;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "BatchEngine", "getNextCommand");
+		exit(1);
+	}
+}
 
 /***********************************************************************/
 /***********************************************************************/
@@ -295,7 +354,17 @@ 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()"; }
@@ -304,6 +373,30 @@ 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
@@ -318,24 +411,13 @@ bool ScriptEngine::getInput(){
 					#ifdef USE_MPI
 						int pid, numProcesses;
 						MPI_Status status; 
-						//MPI_Request request;
 						
 						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
 						MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); 
-						
-						if ((pid != 0) && (!(cFactory->MPIEnabled(commandName)))) {
-cout << pid << " is waiting " << commandName << endl;						
-							char buf[12];
-							
-							MPI_Recv(buf, 12, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);  //make everyone wait - just in case
-							//MPI_Wait(&request, &status);
-					cout << pid << " received " << buf << endl;
-						}
-						
 					
-cout << pid << " is here " << commandName  << endl;
+//cout << pid << " is here " << commandName  << endl;
 						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
-							cout << pid << " is in execute" << endl;	
+							//cout << pid << " is in execute" << endl;	
 					#endif
 					//executes valid command
 					Command* command = cFactory->getCommand(commandName, options);
@@ -344,18 +426,7 @@ cout << pid << " is here " << commandName  << endl;
 					mout->executing = false;
 									
 					#ifdef USE_MPI
-					cout << pid << " is done in execute" << endl;
-							if ((pid == 0) && (!(cFactory->MPIEnabled(commandName)))) {
-								char buf[12];
-								strcpy(buf, "command done"); 
-								
-								for(int i = 1; i < numProcesses; i++) { 
-									MPI_Send(buf, 12, MPI_CHAR, i, 2001, MPI_COMM_WORLD); //make everyone wait - just in case
-									//MPI_Wait(&request, &status);
-						cout << pid << " sent " << buf << endl;
-								}
-				cout << pid << " is sending " << endl;
-							}
+					//cout << pid << " is done in execute" << endl;
 						}
 					#endif
 				}else {		
@@ -377,11 +448,6 @@ cout << pid << " is here " << commandName  << endl;
 string ScriptEngine::getNextCommand(string& commandString) {
 	try {
 		
-		#ifdef USE_MPI
-		int ierr = MPI_Barrier(MPI_COMM_WORLD);
-cout << "barrier = " << ierr << endl;
-		#endif
-		
 		string nextcommand = "";
 		int count = 0;