It's not remotely a fair comparison, as typical scientific computing requires high-performance communication to run with any modicum of efficiency. It's not just a matter of scale---the architecture of a machine like this differs dramatically from AWS of a similar size. [Never mind the national security concerns.]
Generally Infiniband [1] or Omni-Path [2] interconnects between the compute nodes - extremely high throughput and low latency communication on the order of 100 Gb/s and 1 microsecond. These problems aren't trillions of completely independent operations which may work for cloud/distributed architecture. For these types of calculations compute node 6523 needs to know the data coming from compute node 2447 in near-realtime to continue working.
