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What version of Rancher are you running? A controller was added to watch the control plane of a downstream cluster and dynamically add tolerations to the agent deployment.

2.6.9 version! We have a taint (own taint or created by ourselves) in a node and want to run agent on that specific nodes. The GitHub issue link which I shjared above has a workaround, is it possible to use that wild card toleration in a deployment manifest or some another way instead of kubectl patch command.

The cluster agent, with few exceptions, runs on the control plane. Node affinities and tolerations are added to the deployment to achieve this goal. Using a taint/toleration will allow the agent to run on the node you want it to, but it won’t always achieve that goal. Node affinities tell Kubernetes that you want a deployment to run on a specific node. I think that is what you’re after. As far as your question of whether a configuration in Rancher allows you to specify an affinity for the cluster agent, I’m not sure. Digging into Rancher’s helm chart is the only way I know to find this out.

thanks Donnie