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I too naively expected your 3 small VMs to fan out evenly. If it were me, I'd explore pod anti-affinity, if it's important to spread them out. I also wonder if you'd get a different result with a deployment having 3 replicas, because in that scenario Kubernetes ostensibly "knows" they're instances of the same application.

There’s no UI for affinity setup. It seems harvester product is very raw yet..

That would be on the pod that represents the VM.