atmega 328p interrupt and timer setup [C/C++] - embedded

Question

I am trying to set up one interrupt and one counter/timer. The interrupt is external, reading low logic from pin. Timer should increment every 100 us and add up to count variable.
I've set up the interrupt, which is working fine however, after setting up a timer, neither interrupt nor timer works. The code is such:
volatile boolean allowCount = false, timerFlag = false;
volatile unsigned int counter;
boolean pulseLow = false;
void setup(){
Serial.begin(9600);
// initialize external pin interrupt.
PCICR = 0b00000010; // 1. PCIE1: Pin Change Interrupt Enable 1
EICRA |= bit (ISC10); // set wanted flags (low logic level causes interrupt)
PCMSK1 = 0b00010000; // Enable Pin Change Interrupt for A4
// TODO Interrupt settings not working together
// initialize Timer1
cli(); // disable global interrupts
TCCR1A = 0; // set entire TCCR1A register to 0
TCCR1B = 0; // same for TCCR1B
// set compare match register to desired timer count:
OCR1A = 0x18;
// turn on CTC mode:
TCCR1B |= (1 << WGM12);
// Set CS10 and CS12 bits for 64 prescaler:
TCCR1B |= (1 << CS10);
TCCR1B |= (1 << CS11);
// enable timer compare interrupt:
TIMSK1 |= (1 << OCIE1A);
}
void loop(){
if (allowCount == true)
{ timer100_uS();
if (counter > 50 && pulseLow == false){
DDRC |= (1 << DDC3 ); // sets bit DDC3 to 1 within register DDRC
//set pin 3(A3) ouput as sourcing Vcc(HIGH)
PORTC |= (1 << PORTC3);
timerReset();
pulseLow = true;
}
if (pulseLow == true){
timer100_uS();
if (counter >= 500){
//set pin3 of port C to LOW (A3);
PORTC &= ~(1 << PORTC3);
pulseLow = false
timerReset();
}
}
// external pin interrupt
ISR(PCINT1_vect){
if (allowCount == false)
allowCount = true;
}
// timer/counter interrupt
ISR (TIMER1_COMPA_vect)
{
if (timerFlag == true){
counter++;
}
}
void timer_100uS(void){
timerFlag = true;
cli();
}
void timerReset(void){
sei();
timerFlag = false;
counter = 0;
}
Value of OCR0A is calculated to be 24 (0x18) with prescaler 64 and 16 MHz processor based on this formula:
OCRn = [ (clock_speed / Prescaler_value) * Desired_time_in_Seconds ] - 1
How to set up different interrupts so that they don't overlap eachother ?
Or better yet, is it possible to set up timer so that it does not use interrupt ?
Thanks for reading !

Answer 1

As I can see, you are using ATMega328 with Arduino libraries. Your problem is that Arduino library internally uses Timer 1 for its internal purposes. Therefore if you add your own interrupt handler for Timer 1, you override Arduino's interrupt handler for Timer 1 which breaks the library.
If you want to stay with Arduino library, use the library also to control the timer: Arduino Timer1

Answer 2

Thank you for answers #old_timer, #klasyc.
Quite late, but I solved it by using timer0 instead of timer1 with following settings in setup:
// initialize external pin interrupt.
PCICR = 0b00000010; // 1. PCIE1: Pin Change Interrupt Enable 1
EICRA |= bit (ISC10); // set wanted flags (falling edge causes interrupt)
PCMSK1 = 0b00001000; // Enable Pin Change Interrupt for A3
TCCR0B = 0;
TCCR0A = 0;
//set CTC mode
TCCR0A = ( 1 << WGM01 );
// set OCR0A value for 1 us counter (OCRxn = (freq/prescaler)*desired_value)-1
OCR0A = 15;
// set compare match counter
TIMSK0 |= (1 << OCIE0A);
//set prescaler
TCCR0B |= ( 1 << CS00);
and outside the loop:
ISR(TIMER0_COMPA_vect){
counter++;
}