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My needs haven't been complicated for what I've been toying with so I've just used the unfancy basic stuff: Docker Swarm's Overlay, Rancher IPsec, and Weave. Overlay is easy, just works, and has good encrypted performance. Rancher IPsec was the same but 200-300Mbps less on throughput. Weave with fast data path equals that of Rancher IPsec. If you enable encryption though throughput currently drops like a rock. Down to 200Mbps in the same environment. They've worked on that by using IPsec underneath for the encryption on fast data path but it hasn't been released yet.
I haven't touched Flannel or Calico, I just don't need that level of control of complexity.