Earlier quoted context omitted.
You've a good point about the EMR charge - that's easy to overlook. I took a look at Whirr [1] but I don't see how having a cloud-agnostic platform helps - are there really alternatives to EMR out there? Can they give me 500+ cc2.8xlarge equivalent machines on-demand but at spot prices? [1] Assuming this is the Whirr to which you refer: https://whirr.apache.org/
Whirr just uses the AWS APIs to provision a cluster for you, but then you're getting a cluster built on EC2 instances rather than EMR, so you don't pay that EMR overhead. You can choose spot or ondemand instances. If your spots get reaped, I think it would fail pretty similarly to an EMR cluster built on spots. I have no idea how quickly it could provision a 500 node cluster, however.
Thanks for the tip!