Final post

I finally finish the coding. Here are the codes after I modified from an example.

#define numberOfRows 3
#define numberOfColumns 3
#define numberOfLayers 3
#define numberOfAnodes numberOfRows*numberOfColumns
#define nonUsedAnodes 7
#define nonUsedCathodes 5

int serialAn = 41;
int rclkAn = 39;
int srclkAn = 37;
int srclrAn = 35;

int serialAn1 = 33;
int rclkAn1 = 31;
int srclkAn1 = 29;
int srclrAn1 = 27;

int serialCat = 8;
int rclkCat = 6;
int srclkCat = 4;
int srclrCat = 2;


void setup(){
  //anodes  
  pinMode(serialAn, OUTPUT);
  pinMode(rclkAn, OUTPUT);
  pinMode(srclkAn, OUTPUT);
  pinMode(srclrAn, OUTPUT);
  pinMode(serialAn1, OUTPUT);
  pinMode(rclkAn1, OUTPUT);
  pinMode(srclkAn1, OUTPUT);
  pinMode(srclrAn1, OUTPUT);
  
  //cathodes
  pinMode(serialCat, OUTPUT);
  pinMode(rclkCat, OUTPUT);
  pinMode(srclkCat, OUTPUT);
  pinMode(srclrCat, OUTPUT);
  
  //clearing out the registers
  digitalWrite(srclkAn, LOW);
  digitalWrite(serialAn, LOW);
  digitalWrite(srclrAn, HIGH);
  digitalWrite(rclkAn, LOW);
  digitalWrite(srclrAn, LOW);
  digitalWrite(rclkAn, HIGH);
  digitalWrite(srclrAn, HIGH);
  
  digitalWrite(srclkAn1, LOW);
  digitalWrite(serialAn1, LOW);
  digitalWrite(srclrAn1, HIGH);
  digitalWrite(rclkAn1, LOW);
  digitalWrite(srclrAn1, LOW);
  digitalWrite(rclkAn1, HIGH);
  digitalWrite(srclrAn1, HIGH); 
  
  digitalWrite(srclkCat, LOW);
  digitalWrite(serialCat, LOW);
  digitalWrite(srclrCat, HIGH);
  digitalWrite(rclkCat, LOW);
  digitalWrite(srclrCat, LOW);
  digitalWrite(rclkCat, HIGH);
  digitalWrite(srclrCat, HIGH);
 
}

void loop(){

  for(int i=1; i<=numberOfColumns; i++){
    for(int j=1; j<=numberOfRows; j++){
      for(int k=1; k<=numberOfLayers; k++){
        lightUpOneLed(j,i,k,100);
        }
      }
    } 

}


int offLed;
int onLed;

void lightUpOneLed(int anodeRow, int anodeCol, int cathodeLayer, int lightDuration){
  int anodeNumber= (anodeRow*3-3)+anodeCol;
  //turning on the specific anode
  digitalWrite(rclkAn1, LOW);
  digitalWrite(rclkAn, LOW);
  for(offLed=0; offLed<(nonUsedAnodes+anodeNumber-1) && offLed<8; offLed++){
    digitalWrite(serialAn1, LOW);
    digitalWrite(srclkAn1, HIGH);
    digitalWrite(srclkAn1, LOW);
    }
  for(onLed=0; onLed<(2-anodeNumber); onLed++){
    digitalWrite(serialAn1, HIGH);
    digitalWrite(srclkAn1, HIGH);
    digitalWrite(srclkAn1, LOW);
    }
  for(offLed=0; offLed<(anodeNumber-2); offLed++){
    digitalWrite(serialAn, LOW);
    digitalWrite(srclkAn, HIGH);
    digitalWrite(srclkAn, LOW);
    }
  for(onLed=0; onLed<1 && onLed<(anodeNumber-1); onLed++){
    digitalWrite(serialAn, HIGH);
    digitalWrite(srclkAn, HIGH);
    digitalWrite(srclkAn, LOW);
    }
  for(offLed=0; offLed<(numberOfAnodes-anodeNumber); offLed++){
    digitalWrite(serialAn, LOW);
    digitalWrite(srclkAn, HIGH);
    digitalWrite(srclkAn, LOW);
    }
  digitalWrite(rclkAn1, HIGH);
  digitalWrite(rclkAn, HIGH);
  
  //turning on the specific cathode layer
  digitalWrite(rclkCat, LOW);
  for(offLed=0; offLed<(cathodeLayer-1); offLed++){
    digitalWrite(serialCat, HIGH);
    digitalWrite(srclkCat, HIGH);
    digitalWrite(srclkCat, LOW);
    }
  for(onLed=0; onLed<1; onLed++){
    digitalWrite(serialCat, LOW);
    digitalWrite(srclkCat, HIGH);
    digitalWrite(srclkCat, LOW);
    }
  for(offLed=0; offLed<((numberOfLayers-cathodeLayer)+nonUsedCathodes); offLed++){
    digitalWrite(serialCat, HIGH);
    digitalWrite(srclkCat, HIGH);
    digitalWrite(srclkCat, LOW);
    }
  digitalWrite(rclkCat, HIGH);
  delay(lightDuration);

}//end of lightUpOneLed function

The good news is all the LED I had on my breadboard are working and the LEDs were blinking the way as I expected.  But the bad news is I think somehow I messed up, my arduino shut down on itself. Once I unplug the USB and re-connect it. Only few LED went on but in few second my Arduino board shut down again. One solution is I think it drives too much current somehow and few LEDs are over heated. I honestly don't really know why. I would love if someone can help me and fix it.I totally cannot capture a picture well because the board just shut down so fast. Right now, my board just won't turn on at all. So I played around with it for a few moment. I could smell that something was burning. Once I unplugged few wires. Some LEDs started lighting up brightly. That helps me realize that since I have LEDs at the moment, it cannot handle all the current I drove for it.