Interrupts and stepper motor advice needed.

Forum 2005-2010 (read only) Software Troubleshooting
7

A few corrections...

[glow]volatile[/glow] long timer=0;

ISR(TIMER1_COMPA_vect)  // Timer-1 OC1A Match interrupt handler
{
[glow]/* Remove.  This serves no purpose.  Interrupts are disabled when an ISR is called.
  cli();
*/[/glow]
  timer = micros();
  TCNT1 = 0;
  TIMSK1 = 1<<OCIE1A;
};

void loop()
{
  delay(1000);
[glow]/* Accessing timer without first disabling interrupts is not safe.
  Serial.println(timer);
*/[/glow]
}

I believe you're also missing SLI (interrupts enable command) at the end of the interrupt handler

This is not necessary. Reenabling interrupts is automatically performed.