X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=7bcb4e41185bfa2104b3ef29432db0af7cbe58a2;hb=2431fce75705f16d6d7cab7a6f5fe02051d82ca5;hp=5e9ac5f36372a5bdbd4da64d1a87d3bac57b5954;hpb=182db2b6f1747bc1e0b8cd3eceec8751abdd31d5;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 5e9ac5f..7bcb4e4 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -51,10 +51,13 @@ bool InteractEngine::getInput(){
 		
 		while(quitCommandCalled != 1){
 
+
 			mout->mothurOutEndLine();
 			
 			input = getCommand();	
-			mout->mothurOutEndLine();		
+			mout->mothurOutEndLine();	
+		
+			if (mout->control_pressed) { input = "quit()"; }
 			
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
@@ -65,16 +68,27 @@ bool InteractEngine::getInput(){
 			options = parser.getOptionString();
 			
 			if (commandName != "") {
-			
-				//executes valid command
-				Command* command = cFactory->getCommand(commandName, options);
-				quitCommandCalled = command->execute();
-				mout->control_pressed = 0;
-				
-			}else {
-				mout->mothurOut("Your input contains errors. Please try again."); 
-				mout->mothurOutEndLine();
-			}
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+ 
+//cout << pid << " is here " << commandName << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					#endif
+					//executes valid command
+					Command* command = cFactory->getCommand(commandName, options);
+					quitCommandCalled = command->execute();
+					mout->control_pressed = 0;
+					mout->executing = false;
+										
+					#ifdef USE_MPI
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
 		}	
 		return 1;
 	}
@@ -86,6 +100,10 @@ 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
 				char* nextCommand = NULL;
@@ -94,7 +112,7 @@ string Engine::getCommand()  {
 				if(nextCommand != NULL) {  add_history(nextCommand);  }	
 				else{ //^D causes null string and we want it to quit mothur
 					nextCommand = "quit"; 
-					cout << nextCommand << endl;
+					mout->mothurOut(nextCommand);
 				}	
 				
 				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
@@ -104,17 +122,19 @@ string Engine::getCommand()  {
 				mout->mothurOut("mothur > ");
 				getline(cin, nextCommand);
 				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+				
 				return nextCommand;
 			#endif
 		#else
-			string nextCommand = "";
-			mout->mothurOut("mothur > ");
-			getline(cin, nextCommand);
-			mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
-			return nextCommand;
+				string nextCommand = "";
+				
+				mout->mothurOut("mothur > ");
+				getline(cin, nextCommand);
+				mout->mothurOutJustToLog(toString(nextCommand));
+				
+				return nextCommand;
 		#endif
-		
-		mout->mothurOutEndLine();
+	
 						
 	}
 	catch(exception& e) {
@@ -159,18 +179,19 @@ bool BatchEngine::getInput(){
 		
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
-	
+	    int count = 0;
 		while(quitCommandCalled == 0){
 	
-			if (inputBatchFile.eof()) { input = "quit()"; }
-			else { input = getline(inputBatchFile); }
+			input = getNextCommand(inputBatchFile);
+			count++;
 			
 			if (input[0] != '#') {
 				
 				mout->mothurOutEndLine();
 				mout->mothurOut("mothur > " + input);
 				mout->mothurOutEndLine();
-				
+							
+				if (mout->control_pressed) { input = "quit()"; }
 				
 				//allow user to omit the () on the quit command
 				if (input == "quit") { input = "quit()"; }
@@ -180,11 +201,23 @@ bool BatchEngine::getInput(){
 				options = parser.getOptionString();
 										
 				if (commandName != "") {
-
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						
+//cout << pid << " is here " << commandName << '\t' << count << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					#endif
 					//executes valid command
 					Command* command = cFactory->getCommand(commandName, options);
 					quitCommandCalled = command->execute();
 					mout->control_pressed = 0;
+					mout->executing = false;
+										
+					#ifdef USE_MPI
+						}
+					#endif
 				}else {		
 					mout->mothurOut("Invalid."); 
 					mout->mothurOutEndLine();
@@ -202,7 +235,27 @@ bool BatchEngine::getInput(){
 		exit(1);
 	}
 }
-
+/***********************************************************************/
+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()"; }
+		else { nextcommand = getline(inputBatchFile); }
+		
+		return nextcommand;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "BatchEngine", "getNextCommand");
+		exit(1);
+	}
+}
 
 /***********************************************************************/
 /***********************************************************************/
@@ -246,11 +299,11 @@ bool ScriptEngine::getInput(){
 			
 			if (input == "") { input = "quit()"; }
 			
-			
 			mout->mothurOutEndLine();
 			mout->mothurOut("mothur > " + input);
 			mout->mothurOutEndLine();
-
+			
+			if (mout->control_pressed) { input = "quit()"; }
 				
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
@@ -260,15 +313,33 @@ bool ScriptEngine::getInput(){
 			options = parser.getOptionString();
 										
 			if (commandName != "") {
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid, numProcesses;
+						MPI_Status status; 
+						
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); 
+					
+//cout << pid << " is here " << commandName  << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+							//cout << pid << " is in execute" << endl;	
+					#endif
+					//executes valid command
+					Command* command = cFactory->getCommand(commandName, options);
+					quitCommandCalled = command->execute();
+					mout->control_pressed = 0;
+					mout->executing = false;
+									
+					#ifdef USE_MPI
+					//cout << pid << " is done in execute" << endl;
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
 
-				//executes valid command
-				Command* command = cFactory->getCommand(commandName, options);
-				quitCommandCalled = command->execute();
-				mout->control_pressed = 0;
-			}else {		
-				mout->mothurOut("Invalid."); 
-				mout->mothurOutEndLine();
-			}
 			
 		}
 		
@@ -282,6 +353,11 @@ bool ScriptEngine::getInput(){
 /***********************************************************************/
 string ScriptEngine::getNextCommand(string& commandString) {
 	try {
+		
+		#ifdef USE_MPI
+			MPI_Barrier(MPI_COMM_WORLD);
+		#endif
+		
 		string nextcommand = "";
 		int count = 0;
 		
@@ -306,7 +382,7 @@ string ScriptEngine::getNextCommand(string& commandString) {
 				if (commandString.length() == 0) {  break;  }
 			}
 		}
-					
+		
 		return nextcommand;
 	}
 	catch(exception& e) {