latest version

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index 3bdc484ac64a0a1140feee90e299696c2eb292c3..acd417cd8477516f2a670f6a34257964d6c442c3 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -67,16 +67,40 @@ bool InteractEngine::getInput(){
                        options = parser.getOptionString();
                        
                        if (commandName != "") {
-                               mout->executing = true;
-                               //executes valid command
-                               Command* command = cFactory->getCommand(commandName, options);
-                               quitCommandCalled = command->execute();
-                               mout->control_pressed = 0;
-                               mout->executing = false;
-                       }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); 
+                                               
+                                               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)) {
+                                       #endif
+                                       //executes valid command
+                                       Command* command = cFactory->getCommand(commandName, options);
+                                       quitCommandCalled = command->execute();
+                                       mout->control_pressed = 0;
+                                       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 {         
+                                       mout->mothurOut("Invalid."); 
+                                       mout->mothurOutEndLine();
+                               }
                }       
                return 1;
        }
@@ -96,7 +120,7 @@ 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));
@@ -106,17 +130,19 @@ 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) {
@@ -172,7 +198,7 @@ bool BatchEngine::getInput(){
                                mout->mothurOutEndLine();
                                mout->mothurOut("mothur > " + input);
                                mout->mothurOutEndLine();
-                               
+                                                       
                                if (mout->control_pressed) { input = "quit()"; }
                                
                                //allow user to omit the () on the quit command
@@ -184,11 +210,35 @@ bool BatchEngine::getInput(){
                                                                                
                                if (commandName != "") {
                                        mout->executing = true;
+                                       #ifdef USE_MPI
+                                               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)) {
+                                       #endif
                                        //executes valid command
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
                                        mout->control_pressed = 0;
                                        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 {         
                                        mout->mothurOut("Invalid."); 
                                        mout->mothurOutEndLine();
@@ -250,11 +300,10 @@ 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
@@ -265,16 +314,55 @@ bool ScriptEngine::getInput(){
                        options = parser.getOptionString();
                                                                                
                        if (commandName != "") {
-                               mout->executing = true;
-                               //executes valid command
-                               Command* command = cFactory->getCommand(commandName, options);
-                               quitCommandCalled = command->execute();
-                               mout->control_pressed = 0;
-                               mout->executing = false;
-                       }else {         
-                               mout->mothurOut("Invalid."); 
-                               mout->mothurOutEndLine();
-                       }
+                                       mout->executing = true;
+                                       #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;
+                                               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;
+                                                       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;
+                                                       }
+                                               }
+                                       #endif
+                               }else {         
+                                       mout->mothurOut("Invalid."); 
+                                       mout->mothurOutEndLine();
+                               }
+
                        
                }
                
@@ -288,6 +376,12 @@ bool ScriptEngine::getInput(){
 /***********************************************************************/
 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;
                
@@ -312,7 +406,7 @@ string ScriptEngine::getNextCommand(string& commandString) {
                                if (commandString.length() == 0) {  break;  }
                        }
                }
-                                       
+               
                return nextcommand;
        }
        catch(exception& e) {