Patch CoreDNS command is giving error

Please follow the below steps to troubleshoot your error:

Step 1. Execute kubectl describe deploy coredns -n kube-system and check the Pod template section. Does it show something like:

Pod Template:
  Labels:           eks.amazonaws.com/component=coredns
                    k8s-app=kube-dns
  Annotations:      eks.amazonaws.com/compute-type: ec2
   Service Account:  coredns

if there is annotations field in the deployment please execute the command:

kubectl patch deployment coredns \ -n kube-system \ --type json \ -p='[{"op": "remove", "path": "/spec/template/metadata/annotations/eks.amazonaws.com~1compute-type"}]'

If there if no annotation field like below:

Pod Template:
  Labels:           eks.amazonaws.com/component=coredns
                    k8s-app=kube-dns
  Service Account:  coredns

then proceed to step 2 as executing the patch command again will result in error as we are trying to remove the annotations field from the deployment which does not exist.

Step 2 - Execute - k describe pod <your-coredns-podname> -n kube-system and look for Events field, i.e. Is it showing something like below?

Events:
  Type     Reason            Age               From               Message
  ----     ------            ----              ----               -------
  Warning  FailedScheduling  41s (x2 over 6m)  default-scheduler  no nodes available to schedule pods

Based on the error above, you will be able to find the reason of why coredns pods are not able to schedule.

If suppose the error is something similar to above, please create a fargate profile to target coredns pods like this below (replace my-cluster with your cluster name, 111122223333 with your account ID, AmazonEKSFargatePodExecutionRole with the name of your Pod execution role, and 0000000000000001, 0000000000000002, and 0000000000000003 with the IDs of your private subnets. If you don't have a Pod execution role, you must create one first. ):

aws eks create-fargate-profile \
    --fargate-profile-name coredns \
    --cluster-name my-cluster \
    --pod-execution-role-arn arn:aws:iam::111122223333:role/AmazonEKSFargatePodExecutionRole \
    --selectors namespace=kube-system,labels={k8s-app=kube-dns} \
    --subnets subnet-0000000000000001 subnet-0000000000000002 subnet-0000000000000003

If you are not able to troubleshoot based on the above, please let me know and I would be happy to help based on your comments.

Thanks, Manish