1.12.1

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index acd417cd8477516f2a670f6a34257964d6c442c3..7bacec5c0e757c7b77d3c8801970c17bd3cc5a4a 100644 (file)
--- 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;