Try adding the timer variable and clearing that one instead of the ctimer. (Not tested)
App.Controller = Ember.ObjectController.extend({
timer: null,
timerStart: function () {
this.timer = setInterval(this.ctimer, 1000);
},
timerEnd: function () {
this.clearInterval(this.timer);
},
ctimer: function () {
var d = new Date();
document.getElementById("timeBar").innerHTML = d.toLocaleTimeString();
},
});