//Timer interrupt:
#include <avr/io.h>        //for timer2 interrupt to read buttons
#include <avr/interrupt.h> //for timer2 interrupt to read buttons
const byte timer2Match=249; //249 = period of 1.000 ms @prescaler 64, clock 16 MHz
volatile word counter=0;
word counterTop=300-1;
volatile bool ledOn=LOW;

//ISR(TIMER2_OVF_vect) {
ISR(TIMER2_COMPA_vect) { //called once every 1.000 ms
  counter++;
  if (counter==1000) counter=0;
  if (counter==0) ledOn=HIGH;
  if (counter==counterTop) ledOn=LOW;
  digitalWrite(LED_BUILTIN,ledOn); //works well with counterTop=0
}

void setup() {
  Serial.begin(9600);
  pinMode(LED_BUILTIN,OUTPUT);
  
  //Setup timer2 interrupt for buttons:
  cli(); //disable interrupts
  TCCR2A=0; TCCR2B=0; //reset control registers A and B
  TCNT2=0; //initialize counter value to 0
  OCR2A=timer2Match; //set compare match register
  TCCR2A=1<<WGM21; //set mode to CTC
  TCCR2B=1<<CS22; //set prescaler to 64
  TIMSK2=1<<OCIE2A; //enable timer compare interrupt
  //TIMSK2=1<<TOIE2; //timer2 overflow interrupt enable
  sei(); //enable interrupts
}

void loop() {
  while (Serial.available() > 0) {
    counterTop = Serial.parseInt();
  }
  unsigned int counterCopy;
  cli();
  counterCopy=counter;
  sei();

  Serial.print("counter: ");
  Serial.print(counterCopy);
  Serial.print(", counterTop: ");
  Serial.println(counterTop);
  delay(100);
}