Lesson 11: Migrating Node 3 to Cluster B
Migrating from k3s to RKE2 / Migrating Nodes to the New Cluster
Node 3 is the first node we move from Cluster A to Cluster B. The process involves analyzing what runs on the node, creating backups, draining it from the k3s cluster, reinstalling the OS, and joining it to RKE2. Every subsequent node migration follows this same pattern, so this lesson covers each step in detail.
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This is the 11th lesson of the guide Migrating from k3s to RKE2. Make sure you have completed the previous lesson before continuing here. The full list of lessons in the guide can be found in the overview.
When we drain a node, Kubernetes evicts all pods and marks the node as unschedulable. Pods managed by controllers (Deployments, StatefulSets, DaemonSets) are recreated on other nodes automatically. Standalone pods without controllers are deleted permanently.
The drain happens in three stages:
- Cordon marks the node as unschedulable so no new pods land on it
- Evict sends termination signals to all pods, respecting Pod Disruption Budgets
- Reschedule: controllers recreate evicted pods on remaining nodes
Several factors can block or complicate a drain. Pod Disruption Budgets may prevent eviction if removing a pod would violate availability guarantees. Pods with local storage will not migrate their data automatically. Single-replica deployments experience brief unavailability between eviction and rescheduling on another node. Understanding these factors before running the drain command prevents surprises during the migration.
Every cluster is different. The workloads running on Node 3 depend on the applications deployed, scheduling constraints, and how pods were distributed. The commands below provide general guidance for discovering what needs attention before draining.
Start by listing all pods scheduled on Node 3:
$ export KUBECONFIG=/path/to/cluster-a-kubeconfig
$ kubectl get pods -A -o wide --field-selector spec.nodeName=node3
NAMESPACE NAME READY STATUS NODE
default web-app-7d4b8c6f9-x2k9p 1/1 Running node3
monitoring prometheus-0 1/1 Running node3
kube-system canal-node3 1/1 Running node3
DaemonSet pods like canal run on every node and are recreated automatically.
Application pods managed by a Deployment or StatefulSet are rescheduled to other nodes.
StatefulSets may have ordered shutdown requirements, so identify them first:
$ kubectl get statefulsets -A
NAMESPACE NAME READY AGE
database postgres 1/1 30d
monitoring prometheus 1/1 15d
If a StatefulSet pod runs on Node 3, Kubernetes recreates it on another node. For databases, verify replication is healthy before proceeding.
Pods with local storage (hostPath or emptyDir volumes) will not carry their data to the new node:
$ kubectl get pods -A -o jsonpath='{range .items[*]}{.metadata.namespace}/{.metadata.name}: {.spec.volumes[*].name}{"\n"}{end}' | grep -E "local|hostPath"
monitoring/prometheus-0: data local-storage config
Back up any important data from these pods before draining.
Pod Disruption Budgets can block the drain entirely:
$ kubectl get pdb -A
NAMESPACE NAME MIN AVAILABLE MAX UNAVAILABLE ALLOWED DISRUPTIONS
default web-app 2 N/A 1
database postgres 1 N/A 0
If ALLOWED DISRUPTIONS is 0, the drain will wait or fail.
We may need to temporarily relax the PDB or ensure enough replicas are running on other nodes first.
Single-replica deployments cause brief unavailability during the transition:
$ kubectl get deployments -A -o jsonpath='{range .items[*]}{.metadata.namespace}/{.metadata.name}: {.spec.replicas}{"\n"}{end}' | grep ": 1$"
default/backend-api: 1
tools/cron-runner: 1
These workloads are unavailable between eviction and rescheduling, typically seconds to minutes.
Confirm that the remaining nodes have enough headroom to absorb Node 3’s workloads:
$ kubectl top nodes
NAME CPU(cores) CPU% MEMORY(bytes) MEMORY%
node1 450m 11% 2100Mi 26%
node2 380m 9% 1800Mi 22%
node3 520m 13% 2400Mi 30%
After draining Node 3, its workloads shift to Nodes 1 and 2. Both CPU and memory utilization should stay below 80% after absorbing the additional load.
Create an etcd snapshot on the k3s control plane node before making any changes:
# On Node 1 (k3s control plane)
$ ssh root@node1
$ sudo k3s etcd-snapshot save --name pre-node3-migration-$(date +%Y%m%d-%H%M%S)
$ sudo k3s etcd-snapshot ls
For applications with persistent data, create application-level backups as well:
# Example: PostgreSQL database
$ kubectl exec -n <namespace> <pod-name> -- pg_dump -U postgres > backup.sql
# Or use Velero if available
$ velero backup create pre-migration-backup
Mark Node 3 as unschedulable:
$ kubectl cordon node3
$ kubectl get nodes
The output shows SchedulingDisabled for Node 3:
NAME STATUS ROLES AGE VERSION
node1 Ready master 30d v1.28.5+k3s1
node2 Ready <none> 30d v1.28.5+k3s1
node3 Ready,SchedulingDisabled <none> 30d v1.28.5+k3s1
In a separate terminal, watch for pod transitions:
$ watch -n 2 'kubectl get pods -A -o wide | grep -E "node3|Terminating|Pending|ContainerCreating"'
$ kubectl drain node3 \
--ignore-daemonsets \
--delete-emptydir-data \
--grace-period=300 \
--timeout=600s
| Flag | Purpose |
|---|---|
--ignore-daemonsets |
Skip DaemonSet pods (they are removed with the node) |
--delete-emptydir-data |
Allow eviction of pods using emptyDir volumes |
--grace-period=300 |
Give pods 5 minutes to shut down gracefully |
--timeout=600s |
Fail if drain does not complete in 10 minutes |
DaemonSet pods are a special case.
The --ignore-daemonsets flag tells the drain to skip them since they are meant to run on every node and are cleaned up when the node is removed.
If a PDB is blocking eviction, check which one is responsible and, if safe, temporarily reduce the minimum:
# Check which PDB is blocking
$ kubectl get pdb -A
# If safe, temporarily reduce the minimum (restore after drain)
$ kubectl patch pdb <name> -n <namespace> -p '{"spec":{"minAvailable":0}}'
If pods are stuck in Terminating state, force-delete them as a last resort:
# Find stuck pods
$ kubectl get pods -A --field-selector spec.nodeName=node3 | grep Terminating
# Force delete if necessary (may lose in-flight data)
$ kubectl delete pod <pod-name> -n <namespace> --grace-period=0 --force
Pods with hostPath or local-path-provisioner volumes may also block the drain.
Back up any important data, then use --force or delete the pod manually.
# Should show only DaemonSet pods or be empty
$ kubectl get pods -A -o wide --field-selector spec.nodeName=node3
# Verify workloads are running elsewhere
$ kubectl get pods -A | grep -v Running | grep -v Completed
$ kubectl delete node node3
$ kubectl get nodes
$ ssh root@node3
$ sudo systemctl stop k3s-agent
$ sudo systemctl disable k3s-agent
The setup follows the same process as Node 4. The full details for each step are covered in the referenced lessons. This section lists every command needed to get Node 3 ready.
Boot into the Hetzner Rescue System and run the installer. We cover the full walkthrough in Lesson 2.
$ installimage
Select Rocky Linux 10, set the hostname to node3, and use a simple partition layout without swap:
PART /boot ext3 1024M
PART / ext4 all
After installation completes, reboot into the new OS:
$ reboot
Reconnect via SSH (accept the new host key) and harden the server:
# Change the root password
$ passwd
# Update all packages
$ dnf update -y
# Create a dedicated admin user
$ useradd k8sadmin
$ passwd k8sadmin
$ usermod -aG wheel k8sadmin
From the local machine, set up SSH key authentication:
$ ssh-keygen -t ed25519 -f ~/.ssh/node3_k8sadmin_ed25519
$ ssh-copy-id -i ~/.ssh/node3_k8sadmin_ed25519 k8sadmin@<node3-public-ip>
Add an entry to ~/.ssh/config:
# ~/.ssh/config
Host node3
HostName <node3-public-ip>
User k8sadmin
IdentityFile ~/.ssh/node3_k8sadmin_ed25519
IdentitiesOnly yes
Disable root login:
$ sudo vi /etc/ssh/sshd_config
# Set: PermitRootLogin no
$ sudo systemctl restart sshd
$ sudo timedatectl set-timezone Europe/Helsinki
$ sudo hostnamectl set-hostname node3
$ sudo dnf install -y \
vim \
git \
bash-completion \
tar \
unzip \
net-tools \
bind-utils \
jq \
wireguard-tools
$ sudo dnf config-manager --add-repo https://pkgs.tailscale.com/stable/fedora//tailscale.repo
$ sudo dnf install -y tailscale
$ sudo systemctl enable --now tailscaled
$ sudo tailscale up
Configure the VLAN interface with both IPv4 and IPv6 addresses. We cover the full networking walkthrough in Lesson 3.
# Replace enp35s0 with the actual interface name
$ sudo nmcli connection add \
type vlan \
con-name vswitch0 \
dev enp35s0 \
id 4000 \
ipv4.method manual \
ipv4.addresses 10.1.0.13/16 \
ipv4.routes "10.0.0.0/24 10.1.0.1" \
ipv6.method manual \
ipv6.addresses fd00::13/64
$ sudo nmcli connection up vswitch0
If a vswitch0 connection already exists, use modify instead of add:
$ sudo nmcli connection modify vswitch0 \
ipv4.method manual \
ipv4.addresses 10.1.0.13/16 \
ipv4.routes "10.0.0.0/24 10.1.0.1" \
ipv6.method manual \
ipv6.addresses fd00::13/64
$ sudo nmcli connection up vswitch0
Configure public IPv6 on the main interface:
# Replace the address with the assigned IPv6 from Hetzner
$ sudo nmcli connection modify "Wired connection 1" \
ipv6.method manual \
ipv6.addresses "2a01:4f9:XX:XX::2/64" \
ipv6.gateway "fe80::1"
$ sudo nmcli connection up "Wired connection 1"
Enable IPv6 forwarding:
$ sudo tee /etc/sysctl.d/99-ipv6-forward.conf <<EOF
net.ipv6.conf.all.forwarding = 1
net.ipv6.conf.default.forwarding = 1
EOF
$ sudo sysctl -p /etc/sysctl.d/99-ipv6-forward.conf
Configure the Hetzner Robot firewall for Node 3 with the same rules as Node 4. We cover rule explanations and verification steps in Lesson 4.
| ID | Name | Version | Protocol | Source IP | Source Port | Dest Port | TCP Flags | Action |
|---|---|---|---|---|---|---|---|---|
| #1 | vswitch | ipv4 | * | 10.0.0.0/8 | accept | |||
| #2 | tcp established | ipv4 | tcp | 1024-65535 | ack | accept | ||
| #3 | tcp established-v6 | ipv6 | tcp | 1024-65535 | ack | accept | ||
| #4 | dns responses | ipv4 | udp | 53 | 1024-65535 | accept | ||
| #5 | ssh | * | tcp | 22 | accept |
$ ping -c 3 10.1.0.14
PING 10.1.0.14 (10.1.0.14) 56(84) bytes of data.
64 bytes from 10.1.0.14: icmp_seq=1 ttl=64 time=0.486 ms
64 bytes from 10.1.0.14: icmp_seq=2 ttl=64 time=0.353 ms
64 bytes from 10.1.0.14: icmp_seq=3 ttl=64 time=0.413 ms
--- 10.1.0.14 ping statistics ---
3 packets transmitted, 3 received, 0% packet loss, time 2086ms
rtt min/avg/max/mdev = 0.353/0.417/0.486/0.054 ms
$ ping6 -c 3 fd00::14
PING fd00::14 (fd00::14) 56 data bytes
64 bytes from fd00::14: icmp_seq=1 ttl=64 time=0.508 ms
64 bytes from fd00::14: icmp_seq=2 ttl=64 time=0.358 ms
64 bytes from fd00::14: icmp_seq=3 ttl=64 time=0.388 ms
--- fd00::14 ping statistics ---
3 packets transmitted, 3 received, 0% packet loss, time 2084ms
rtt min/avg/max/mdev = 0.358/0.418/0.508/0.064 ms
$ nc -zv 10.1.0.14 9345
Ncat: Version 7.92 ( https://nmap.org/ncat )
Ncat: Connected to 10.1.0.14:9345.
Ncat: 0 bytes sent, 0 bytes received in 0.01 seconds.
The last command verifies the RKE2 supervisor port is reachable.
When a new node joins an existing RKE2 cluster, the process differs from bootstrapping the first node.
| Aspect | First Node (Bootstrap) | Additional Nodes (Join) |
|---|---|---|
| Config | Defines cluster settings | References existing cluster |
| etcd | Creates new cluster | Joins existing cluster |
| Certs | Generates CA | Receives certs from server |
| State | Empty | Syncs from existing nodes |
The key configuration difference is the server directive, which tells RKE2 where to register with the existing cluster.
The rke2 server process on Node 4 listens on port 9345 for new nodes to register, while the Kubernetes API remains on port 6443.
On Rocky Linux the install script detects RPM support and installs via dnf automatically:
$ curl -sfL https://get.rke2.io | sudo sh -
$ sudo systemctl enable rke2-server.service
This installs the rke2-server service (the default type) and places additional utilities (kubectl, crictl, and ctr) in /var/lib/rancher/rke2/bin/.
Apply the runc v1.3.4 workaround from Lesson 5 before starting RKE2.
Download the binary to /etc/rancher/rke2/runc-v1.3.4 and create the containerd config template at /var/lib/rancher/rke2/agent/etc/containerd/config-v3.toml.tmpl.
Retrieve the cluster token from Node 4.
RKE2 generated this token during the initial bootstrap and stored it at /var/lib/rancher/rke2/server/node-token:
# On Node 4
$ sudo cat /var/lib/rancher/rke2/server/node-token
K10...::server:xxxx
Back on Node 3, create the configuration directory using the same multi-file layout from Lesson 5:
$ sudo mkdir -p /etc/rancher/rke2/config.yaml.d
The join configuration tells RKE2 where to register and how to authenticate. This file is the only difference between a bootstrap node and a joining node:
# /etc/rancher/rke2/config.yaml.d/00-join.yaml
server: https://10.1.0.14:9345
token: <paste-token-from-node4>
The network configuration mirrors Node 4’s settings with Node 3’s addresses:
# /etc/rancher/rke2/config.yaml.d/10-network.yaml
cni: canal
node-ip: 10.1.0.13,fd00::13
node-external-ip:
- 65.109.XX.XX # Replace with Node 3's public IPv4
- 2a01:4f9:XX:XX::2 # Replace with Node 3's public IPv6
advertise-address: 10.1.0.13
bind-address: 10.1.0.13
cluster-cidr: 10.42.0.0/16,fd00:42::/56
service-cidr: 10.43.0.0/16,fd00:43::/112
cluster-dns: 10.43.0.10
kubelet-arg:
- "resolv-conf=/etc/rancher/rke2/resolv.conf"
Create the clean resolv.conf for kubelet to isolate pod DNS from Tailscale’s MagicDNS on the host, as described in Lesson 6:
$ cat <<'EOF' | sudo tee /etc/rancher/rke2/resolv.conf
nameserver 1.1.1.1
nameserver 1.0.0.1
EOF
The external access configuration adds Node 3’s names and IPs to the API server certificate:
# /etc/rancher/rke2/config.yaml.d/20-external-access.yaml
tls-san:
- node3
- node3.k8s.local
- 10.1.0.13
- fd00::13
- cluster.yourdomain.com
The security configuration is identical to Node 4:
# /etc/rancher/rke2/config.yaml.d/30-security.yaml
secrets-encryption: true
disable:
- rke2-ingress-nginx
etcd-snapshot-schedule-cron: "0 */6 * * *"
etcd-snapshot-retention: 5
Each control plane node runs its own kube-apiserver, so the authentication configuration from Lesson 9 must also be present.
Copy auth-config.yaml from Node 4 and create the corresponding RKE2 config file:
# Copy the AuthenticationConfiguration from Node 4
$ sudo scp node4:/etc/rancher/rke2/auth-config.yaml /etc/rancher/rke2/auth-config.yaml
# /etc/rancher/rke2/config.yaml.d/40-authentication.yaml
kube-apiserver-arg:
- "authentication-config=/etc/rancher/rke2/auth-config.yaml"
$ sudo systemctl start rke2-server.service
$ sudo journalctl -u rke2-server -f
The join process takes several minutes.
The node contacts Node 4’s supervisor API on port 9345, retrieves cluster certificates, joins etcd as a new member, starts control plane components, and syncs existing cluster state.
Watch for these log messages indicating success:
level=info msg="Starting etcd member..."
level=info msg="etcd member started"
level=info msg="Running kube-apiserver..."
Using the kubectl installed with RKE2, check that Node 3 has joined successfully:
$ kubectl get nodes -o wide
Both nodes should appear with dual-stack IPs:
NAME STATUS ROLES AGE VERSION INTERNAL-IP
node3 Ready control-plane,etcd,master 2m v1.34.3+rke2r3 10.1.0.13,fd00::13
node4 Ready control-plane,etcd,master 3h v1.34.3+rke2r3 10.1.0.14,fd00::14
On Node 4, use the etcdctl alias configured in Lesson 5 to verify that Node 3 has joined the etcd cluster:
$ etcdctl member list
xxxx, started, node4-xxxx, https://10.1.0.14:2380, https://10.1.0.14:2379, false
yyyy, started, node3-xxxx, https://10.1.0.13:2380, https://10.1.0.13:2379, false
The output shows two etcd members, confirming the cluster has grown from a single node to a two-member cluster.
Canal automatically deploys to new nodes:
$ kubectl get pods -n kube-system -l k8s-app=canal -o wide
NAME READY STATUS RESTARTS AGE IP NODE NOMINATED NODE READINESS GATES
rke2-canal-6qrrc 2/2 Running 0 7m45s 10.1.0.14 node4 <none> <none>
rke2-canal-ntzcl 2/2 Running 0 7m41s 10.1.0.13 node3 <none> <none>
This is the first time we can verify that WireGuard tunnels actually work. Until now, Node 4 had no peers. Check that both nodes see each other as WireGuard peers with a recent handshake:
$ sudo wg show flannel-wg
interface: flannel-wg
public key: <node3-public-key>
private key: (hidden)
listening port: 51820
peer: <node4-public-key>
endpoint: 10.1.0.14:51820
allowed ips: 10.42.0.0/24
latest handshake: 1 minute, 47 seconds ago
transfer: 727.82 KiB received, 615.54 KiB sent
The endpoint should show a vSwitch IP (10.1.0.x), confirming that WireGuard traffic stays on the private network.
If the endpoint shows a public IP instead, the flannel.regexIface setting from Lesson 6 is not applied. Verify the Canal HelmChartConfig and restart the Canal DaemonSet.
The allowed ips entry shows Node 4’s pod subnet, and the handshake confirms the encrypted tunnel is active.
Test cross-node pod connectivity through the tunnel:
# Ping a pod IP on Node 4 (from the 10.42.0.x range)
$ ping -c 3 10.42.0.8
If pings fail with “Required key not available” or “No route to host”, see the WireGuard troubleshooting section below.
Verify that Cluster A is still healthy with its remaining two nodes:
$ export KUBECONFIG=/path/to/cluster-a-kubeconfig
$ kubectl get nodes
$ kubectl get pods -A | grep -v Running | grep -v Completed
$ kubectl top nodes
Longhorn is already running on the cluster. The HelmChart manifest deployed in Lesson 7 handles that automatically.
However, each new node needs system-level dependencies (iSCSI for block storage and NFSv4 for RWX volumes) before Longhorn can schedule replicas on it.
Install longhornctl and run the preflight installer on Node 3:
$ curl -fL -o /usr/local/bin/longhornctl \
https://github.com/longhorn/cli/releases/download/v1.11.0/longhornctl-linux-amd64
$ chmod +x /usr/local/bin/longhornctl
$ /usr/local/bin/longhornctl --kubeconfig /etc/rancher/rke2/rke2.yaml install preflight
Run the preflight check to confirm all dependencies are in place:
$ /usr/local/bin/longhornctl --kubeconfig /etc/rancher/rke2/rke2.yaml check preflight
The check should report no errors for Node 3. We cover a detailed walkthrough of what each dependency does and how to troubleshoot failures in Lesson 7.
Once the preflight passes, verify that Longhorn recognizes Node 3 as schedulable:
$ kubectl get nodes.longhorn.io -n longhorn-system
NAME READY ALLOWSCHEDULING SCHEDULABLE AGE
node3 True true True 2m
node4 True true True 3h
With two storage nodes, Longhorn can now replicate volumes across nodes.
We increase the replica count once a third node joins the cluster in Lesson 12.
Repeat this longhornctl preflight process on every node that joins the cluster going forward.
If cross-node pod traffic fails with “no route to host” or “Required key not available”, the most likely cause is a Flannel backend mismatch between nodes.
This happens when the existing node is still running the VXLAN backend while the new node picks up the WireGuard configuration from the HelmChartConfig applied in Lesson 6.
The new node creates a flannel-wg interface, but the existing node still uses flannel.1 (VXLAN), so the two nodes cannot exchange pod traffic.
Check which interfaces each node is using:
# On each node
$ ip link show | grep -E "flannel|wg"
18: flannel.1: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1450 qdisc noqueue state UNKNOWN mode DEFAULT group default
23: flannel-v6.1: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1430 qdisc noqueue state UNKNOWN mode DEFAULT group default
87: flannel-wg: <POINTOPOINT,NOARP,UP,LOWER_UP> mtu 1420 qdisc noqueue state UNKNOWN mode DEFAULT group default
88: flannel-wg-v6: <POINTOPOINT,NOARP,UP,LOWER_UP> mtu 1420 qdisc noqueue state UNKNOWN mode DEFAULT group default
If one node shows flannel.1 and the other shows flannel-wg, restart the Canal DaemonSet to align both nodes on the WireGuard backend:
$ kubectl rollout restart ds rke2-canal -n kube-system
$ kubectl rollout status ds rke2-canal -n kube-system --timeout=120s
After the restart, both nodes should show flannel-wg and flannel-wg-v6 interfaces.
Verify the tunnel is established with wg show flannel-wg and look for a peer entry with a recent handshake.
Lesson Conclusion
Congratulations! Node 3 has been migrated from Cluster A to Cluster B, running RKE2 as the second control plane node with etcd showing 2 members. You have completed this lesson and you can now continue with the next one.
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