X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=2ed819f9661fe728526c5e9ba59ba661f58027e9;hb=7837a9bfdfccdc26360987a44c389832fdb82651;hp=b68bf61e4703fbd77133f8ba72c8488a78519d29;hpb=813f0516e9c7533859f57ebe6d7b8854896bf009;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index b68bf61..2ed819f 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -67,27 +67,27 @@ bool InteractEngine::getInput(){
 			options = parser.getOptionString();
 			
 			if (commandName != "") {
-				mout->executing = true;
-				
-				#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-					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("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;
 	}
@@ -99,15 +99,10 @@ bool InteractEngine::getInput(){
 /***********************************************************************/
 string Engine::getCommand()  {
 	try {
-	#ifdef USE_MPI //mpirun doesn't work with readline
-				string nextCommand = "";
-				
-				mout->mothurOut("mothur > ");
-				getline(cin, nextCommand);
-				mout->mothurOutJustToLog(toString(nextCommand));
-				
-				return nextCommand;
-	#else
+		#ifdef USE_MPI
+			MPI_Barrier(MPI_COMM_WORLD);
+		#endif
+	
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 			#ifdef USE_READLINE
 				char* nextCommand = NULL;
@@ -138,7 +133,7 @@ string Engine::getCommand()  {
 				
 				return nextCommand;
 		#endif
-	#endif
+	
 						
 	}
 	catch(exception& e) {
@@ -183,11 +178,11 @@ 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] != '#') {
 				
@@ -209,7 +204,8 @@ bool BatchEngine::getInput(){
 					#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
@@ -217,7 +213,7 @@ bool BatchEngine::getInput(){
 					quitCommandCalled = command->execute();
 					mout->control_pressed = 0;
 					mout->executing = false;
-				
+										
 					#ifdef USE_MPI
 						}
 					#endif
@@ -238,7 +234,27 @@ 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);
+	}
+}
 
 /***********************************************************************/
 /***********************************************************************/
@@ -296,26 +312,33 @@ bool ScriptEngine::getInput(){
 			options = parser.getOptionString();
 										
 			if (commandName != "") {
-				mout->executing = true;
-				#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					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); 
 					
-					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();
-			}
+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();
+				}
+
 			
 		}
 		
@@ -329,6 +352,11 @@ bool ScriptEngine::getInput(){
 /***********************************************************************/
 string ScriptEngine::getNextCommand(string& commandString) {
 	try {
+		
+		#ifdef USE_MPI
+			MPI_Barrier(MPI_COMM_WORLD);
+		#endif
+		
 		string nextcommand = "";
 		int count = 0;
 		
@@ -353,7 +381,7 @@ string ScriptEngine::getNextCommand(string& commandString) {
 				if (commandString.length() == 0) {  break;  }
 			}
 		}
-					
+		
 		return nextcommand;
 	}
 	catch(exception& e) {