+ 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();
+ }