Serial communication and reading byte arrays with Arduino

Shouldn't some of that code be inside of loop()? Specifically, everything but Serial.begin(9600)? Anyway, this code won't work because ackmodule is not defined. Is it supposed to be GetDataACK? It's also a good idea to implement error handling, especially when having to debug, like this:

  if(Serial.available() > 0) {
    received_byte[i] = Serial.read();
    if(received_byte[i++] == -1) {  // no data available
      // error handling
    }
  }

I'm not sure what types the Arduino sketch libraries support, but i can just be an unsigned char (I would call it uint8_t) instead of a full singed 16-bit number (int). As Chris Stratton mentioned, there are better ways to wait for characters; for example the error handling example, or this:

while(Serial.available() < 5) {}; // 5 can be 0 to fetch 1 char at a time

This can be implemented without the library in this form:

char rx()
{
        while ((UCSRA & (1<<RXC)) == 0) {};
        return UDR;
}

... Calling it with something like char nextbyte = rx(). Arduino serial tutorial is here.

If you just want to send the command once at startup, and then read the response you want to do this:

byte GetData[] = {0x02,0x12,0x00}
byte GetDataACK[] = {0x02,0x06,0x06,0x06,0x06,0x06}; 

void setup(){   
  Serial.begin(9600); 
  Serial.write(GetData,sizeof(GetData)); //Send the byte array    
}

void loop(){
  if(Serial.available() > 5) {
    for(int i=0;i<6;i++){
      if(GetDataACK[i]!=Serial.read()){
        // Do something
      }
    }
  }    
}  

Now I'm not sure what you're trying to accomplish with the inner if statement of loop, but it seems kind of backwards to me. Wouldn't you only want to "do something" after you have successfully read the data Ack? I think what you really want is a little state machine:

#define DATA_LENGTH           14 // or whatever the length of your data segment is

#define STATE_IDLE            0
#define STATE_SEND_COMMAND    1
#define STATE_WAITING_FOR_ACK 2
#define STATE_GET_DATA        3

byte GetData[] = {0x02,0x12,0x00}
byte GetDataACK[] = {0x02,0x06,0x06,0x06,0x06,0x06}; 
byte RxData[DATA_LENGTH] = {0};
byte state = STATE_SEND_COMMAND;

void setup(){   
  Serial.begin(9600); 
  state = STATE_SEND_COMMAND;            // redundant
}

void loop(){
  switch(state){
  case STATE_IDLE: break;
  case STATE_SEND_COMMAND:
     Serial.write(GetData,sizeof(GetData)); //Send the byte array             
     state = STATE_WAITING_FOR_ACK;
     break;
  case STATE_WAITING_FOR_ACK:
     if(Serial.available() > 5) {
        for(int i=0;i<6;i++){
           if(GetDataACK[i]!=Serial.read()){
           // ACK doesn't match what you expect
           // you should go to some other state at this point
           // i'll just send you to idle
              state = STATE_IDLE;
              break;
           }
        }
     }
     break;
  case STATE_GET_DATA:
     if(Serial.available() > DATA_LENGTH) {
        for(int i = 0; i < DATA_LENGTH; i++){
           RxData[i] = Serial.read();
        }

        // congratulations you have data in your array
        // presumably now you want to something with it

        // and then switch back to some other state
        // i'll send you back to IDLE :)
        state = STATE_IDLE;
        break;
     }       
  }      
}