Clock speed increases definitely slowed down, but now that software can use parallelism better, we're seeing big wins again. Current desktop/laptop packages are doing 100 trillion operations per second. The article's processor could do one floating point op per cycle, or 1B ops. So, we've seen a 100,000x speedup in the last 25 years. That's a doubling every ~ 1.5 years since 2000.

It's not quite apples-to-apples, of course, due to floating point precision decreasing since then, vectorization, etc, but it's not like progress stopped in 2000!