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We ultimately migrated our Hadoop jobs to Qubole, a rising player in the Hadoop as a Service space. Given that EMR had become unstable at our scale, we had to quickly move to a provider that played well with AWS (specifically, spot instances) and S3. Qubole supported AWS/S3 and was relatively easy to get started on. After vetting Qubole and comparing its performance against alternatives (including managed clusters), we decided to go with Qubole