1.12.1

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index 7bcb4e41185bfa2104b3ef29432db0af7cbe58a2..7bacec5c0e757c7b77d3c8801970c17bd3cc5a4a 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -51,17 +51,50 @@ 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();   
                        mout->mothurOutEndLine();       
-               
+                       
                        if (mout->control_pressed) { input = "quit()"; }
                        
                        //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();
        
@@ -72,9 +105,9 @@ 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);
@@ -100,9 +133,6 @@ 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
@@ -181,10 +211,45 @@ 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();
@@ -239,11 +304,6 @@ 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()"; }
@@ -294,7 +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()"; }
@@ -303,6 +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
@@ -354,10 +448,6 @@ bool ScriptEngine::getInput(){
 string ScriptEngine::getNextCommand(string& commandString) {
        try {
                
-               #ifdef USE_MPI
-                       MPI_Barrier(MPI_COMM_WORLD);
-               #endif
-               
                string nextcommand = "";
                int count = 0;