I suspect the answer is in the networking, what this article spends most of its time talking about. HPC networking is so ridiculously much better than commodity networking. 1us latencies vs 100us+, 200Gbps bandwidth vs 10Gbps. I imagine certain kinds of especially simulations involve a ton of communication between nodes simulating nearby cells and everything is completely bottlenecked on that. It might even be that you can't even match a supercomputer's speed by just buying more AWS instances because the scaling factors on the communication mean more instances doesn't make your sim faster. Again this is mostly inference on my part from things I've read, no first-hand knowledge.