Bottlerocket

How to backup and restore External etcd on Bottlerocket OS

This guide requires some common shell tools such as:

  • grep
  • xargs
  • ssh
  • scp
  • cut

Make sure you have these installed on your admin machine before continuing.

Admin machine environment variables setup

On your admin machine, set the following environment variables that will later come in handy

export MANAGEMENT_CLUSTER_NAME="eksa-management"     # Set this to the management cluster name
export CLUSTER_NAME="eksa-workload"                  # Set this to name of the cluster you want to backup (management or workload)
export SSH_KEY="path-to-private-ssh-key"             # Set this to the cluster's private SSH key path
export SSH_USERNAME="ec2-user"                       # Set this to the SSH username
export SNAPSHOT_PATH="/tmp/snapshot.db"              # Set this to the path where you want the etcd snapshot to be saved

export MANAGEMENT_KUBECONFIG=${MANAGEMENT_CLUSTER_NAME}/${MANAGEMENT_CLUSTER_NAME}-eks-a-cluster.kubeconfig
export CLUSTER_KUBECONFIG=${CLUSTER_NAME}/${CLUSTER_NAME}-eks-a-cluster.kubeconfig
export ETCD_ENDPOINTS=$(kubectl --kubeconfig=${MANAGEMENT_KUBECONFIG} -n eksa-system get machines --selector cluster.x-k8s.io/cluster-name=${CLUSTER_NAME},cluster.x-k8s.io/etcd-cluster=${CLUSTER_NAME}-etcd -ojsonpath='{.items[*].status.addresses[0].address}')
export CONTROL_PLANE_ENDPOINTS=($(kubectl --kubeconfig=${MANAGEMENT_KUBECONFIG} -n eksa-system get machines --selector cluster.x-k8s.io/control-plane-name=${CLUSTER_NAME} -ojsonpath='{.items[*].status.addresses[0].address}'))

Prepare etcd nodes for backup and restore

Install SCP on the etcd nodes:

echo -n ${ETCD_ENDPOINTS} | xargs -I {} -d" " ssh -o StrictHostKeyChecking=no -i ${SSH_KEY} ${SSH_USERNAME}@{} sudo yum -y install openssh-clients

Create etcd Backup

Make sure to setup the admin environment variables and prepare your ETCD nodes for backup before moving forward.

  1. SSH into one of the etcd nodes

    export ETCD_NODE=$(echo -n ${ETCD_ENDPOINTS} | cut -d " " -f1)
ssh -i ${SSH_KEY} ${SSH_USERNAME}@${ETCD_NODE}

  2. Drop into Bottlerocket’s root shell

    sudo sheltie

  3. Set these environment variables

    # get the container ID corresponding to etcd pod
export ETCD_CONTAINER_ID=$(ctr -n k8s.io c ls | grep -w "etcd-io" | head -1 | cut -d " " -f1)

# get the etcd endpoint
export ETCD_ENDPOINT=$(cat /etc/kubernetes/manifests/etcd | grep -wA1 ETCD_ADVERTISE_CLIENT_URLS | tail -1 | grep -oE '[^ ]+$')

  4. Create the etcd snapshot

        ctr -n k8s.io t exec -t --exec-id etcd ${ETCD_CONTAINER_ID} etcdctl \
        --endpoints=${ETCD_ENDPOINT} \
        --cacert=/var/lib/etcd/pki/ca.crt \
        --cert=/var/lib/etcd/pki/server.crt \
        --key=/var/lib/etcd/pki/server.key \
        snapshot save /var/lib/etcd/data/etcd-backup.db
    
        ctr -n k8s.io t exec -t --exec-id etcd ${ETCD_CONTAINER_ID} etcdctl \
        --endpoints=${ETCD_ENDPOINT} \
        --cacert=/var/lib/etcd/pki/ca.crt \
        --cert=/var/lib/etcd/pki/server.crt \
        --key=/var/lib/etcd/pki/server.key \
        snapshot save /var/lib/etcd/data/etcd-backup.db

  5. Move the snapshot to another directory and set proper permissions

    mv /var/lib/etcd/data/etcd-backup.db /run/host-containerd/io.containerd.runtime.v2.task/default/admin/rootfs/home/ec2-user/snapshot.db
chown 1000 /run/host-containerd/io.containerd.runtime.v2.task/default/admin/rootfs/home/ec2-user/snapshot.db

  6. Exit out of etcd node. You will have to type exit twice to get back to the admin machine

    exit
exit

  7. Copy over the snapshot from the etcd node

    scp -i ${SSH_KEY} ${SSH_USERNAME}@${ETCD_NODE}:/home/ec2-user/snapshot.db ${SNAPSHOT_PATH}

You should now have the etcd snapshot in your current working directory.

Restore etcd from Backup

Make sure to setup the admin environment variables and prepare your etcd nodes for restore before moving forward.

  1. Pause cluster reconciliation

    Before starting the process of restoring etcd, you have to pause some cluster reconciliation objects so EKS Anywhere doesn’t try to perform any operations on the cluster while you restore the etcd snapshot.

    kubectl annotate clusters.anywhere.eks.amazonaws.com $CLUSTER_NAME anywhere.eks.amazonaws.com/paused=true --kubeconfig=$MANAGEMENT_KUBECONFIG

kubectl patch clusters.cluster.x-k8s.io $CLUSTER_NAME --type merge -p '{"spec":{"paused": true}}' -n eksa-system --kubeconfig=$MANAGEMENT_KUBECONFIG

  2. Stop control plane core components

    You also need to stop the control plane core components so the Kubernetes API server doesn’t try to communicate with etcd while you perform etcd operations.

    • You can use this command to get the control plane node IPs which you can use to SSH
    echo -n ${CONTROL_PLANE_ENDPOINTS[@]} | xargs -I {} -d " " echo "{}"
    • SSH into the node and stop the core components. You must do this for each control plane node.
    # SSH into the control plane node using the IPs printed in previous command
ssh -i ${SSH_KEY} ${SSH_USERNAME}@<Control Plane IP from previous command>

# drop into bottlerocket root shell
sudo sheltie

# create a temporary directory and move the static manifests to it
mkdir -p /tmp/temp-manifests
mv /etc/kubernetes/manifests/* /tmp/temp-manifests
    • Exit out of the Bottlerocket node
    # exit from bottlerocket's root shell
exit

# exit from bottlerocket node
exit

    Repeat these steps for each control plane node.

  3. Copy the backed-up etcd snapshot to all the etcd nodes

    echo -n ${ETCD_ENDPOINTS} | xargs -I {} -d" " scp -o StrictHostKeyChecking=no -i ${SSH_KEY} ${SNAPSHOT_PATH} ${SSH_USERNAME}@{}:/home/ec2-user

  4. Perform the etcd restore

    For this step, you have to SSH into each etcd node and run the restore command.

    • Get etcd nodes IPs for SSH’ing into the nodes
    # This should print out all the etcd IPs
echo -n ${ETCD_ENDPOINTS} | xargs -I {} -d " " echo "{}"

    # SSH into the etcd node using the IPs printed in previous command
ssh -i ${SSH_KEY} ${SSH_USERNAME}@<etcd IP from previous command>

# drop into bottlerocket\'s root shell
sudo sheltie

# copy over the etcd snapshot to the appropriate location
cp /run/host-containerd/io.containerd.runtime.v2.task/default/admin/rootfs/home/ec2-user/snapshot.db /var/lib/etcd/data/etcd-snapshot.db

# setup the etcd environment
export ETCD_NAME=$(cat /etc/kubernetes/manifests/etcd | grep -wA1 ETCD_NAME | tail -1 | grep -oE '[^ ]+$')
export ETCD_INITIAL_ADVERTISE_PEER_URLS=$(cat /etc/kubernetes/manifests/etcd | grep -wA1 ETCD_INITIAL_ADVERTISE_PEER_URLS | tail -1 | grep -oE '[^ ]+$')
export ETCD_INITIAL_CLUSTER=$(cat /etc/kubernetes/manifests/etcd | grep -wA1 ETCD_INITIAL_CLUSTER | tail -1 | grep -oE '[^ ]+$')
export INITIAL_CLUSTER_TOKEN="etcd-cluster-1"

# get the container ID corresponding to etcd pod
export ETCD_CONTAINER_ID=$(ctr -n k8s.io c ls | grep -w "etcd-io" | head -1 | cut -d " " -f1)

    # run the restore command
ctr -n k8s.io t exec -t --exec-id etcd ${ETCD_CONTAINER_ID} etcdctl \
    snapshot restore /var/lib/etcd/data/etcd-snapshot.db \
    --name=${ETCD_NAME} \
    --initial-cluster=${ETCD_INITIAL_CLUSTER} \
    --initial-cluster-token=${INITIAL_CLUSTER_TOKEN} \
    --initial-advertise-peer-urls=${ETCD_INITIAL_ADVERTISE_PEER_URLS} \
    --cacert=/var/lib/etcd/pki/ca.crt \
    --cert=/var/lib/etcd/pki/server.crt \
    --key=/var/lib/etcd/pki/server.key
    
    # run the restore command
ctr -n k8s.io t exec -t --exec-id etcd ${ETCD_CONTAINER_ID} etcdctl \
    snapshot restore /var/lib/etcd/data/etcd-snapshot.db \
    --name=${ETCD_NAME} \
    --initial-cluster=${ETCD_INITIAL_CLUSTER} \
    --initial-cluster-token=${INITIAL_CLUSTER_TOKEN} \
    --initial-advertise-peer-urls=${ETCD_INITIAL_ADVERTISE_PEER_URLS} \
    --cacert=/var/lib/etcd/pki/ca.crt \
    --cert=/var/lib/etcd/pki/server.crt \
    --key=/var/lib/etcd/pki/server.key
    
    # move the etcd data files out of the container to a temporary location
mkdir -p /tmp/etcd-files
$(ctr -n k8s.io snapshot mounts /tmp/etcd-files/ ${ETCD_CONTAINER_ID})
mv /tmp/etcd-files/${ETCD_NAME}.etcd /tmp/

# stop the etcd pod
mkdir -p /tmp/temp-manifests
mv /etc/kubernetes/manifests/* /tmp/temp-manifests

# backup the previous etcd data files
mv /var/lib/etcd/data/member /var/lib/etcd/data/member.backup

# copy over the new etcd data files to the data directory
mv /tmp/${ETCD_NAME}.etcd/member /var/lib/etcd/data/

# copy the WAL folder for the cluster member data before the restore to the data/member directory
cp -r /var/lib/etcd/data/member.backup/wal /var/lib/etcd/data/member

# re-start the etcd pod
mv /tmp/temp-manifests/* /etc/kubernetes/manifests/
    • Cleanup temporary files and folders
    # clean up all the temporary files
umount /tmp/etcd-files
rm -rf /tmp/temp-manifests /tmp/${ETCD_NAME}.etcd /tmp/etcd-files/ /var/lib/etcd/data/etcd-snapshot.db
    • Exit out of the Bottlerocket node
    # exit from bottlerocket's root shell
exit

# exit from bottlerocket node
exit

    Repeat this step for each etcd node.

  5. Restart control plane core components

    • You can use this command to get the control plane node IPs which you can use to SSH
    echo -n ${CONTROL_PLANE_ENDPOINTS[@]} | xargs -I {} -d " " echo "{}"
    • SSH into the node and restart the core components. You must do this for each control plane node.
    # SSH into the control plane node using the IPs printed in previous command
ssh -i ${SSH_KEY} ${SSH_USERNAME}@<Control Plane IP from previous command>

# drop into bottlerocket root shell
sudo sheltie

# move the static manifests back to the right directory
mv /tmp/temp-manifests/* /etc/kubernetes/manifests/
    • Exit out of the Bottlerocket node
    # exit from bottlerocket's root shell
exit

# exit from bottlerocket node
exit

    Repeat these steps for each control plane node.

  6. Unpause the cluster reconcilers

    Once the etcd restore is complete, you can resume the cluster reconcilers.

    kubectl annotate clusters.anywhere.eks.amazonaws.com $CLUSTER_NAME anywhere.eks.amazonaws.com/paused- --kubeconfig=$MANAGEMENT_KUBECONFIG

kubectl patch clusters.cluster.x-k8s.io $CLUSTER_NAME --type merge -p '{"spec":{"paused": false}}' -n eksa-system --kubeconfig=$MANAGEMENT_KUBECONFIG

At this point you should have the etcd cluster restored to snapshot. To verify, you can run the following commands:

kubectl --kubeconfig=${CLUSTER_KUBECONFIG} get nodes

kubectl --kubeconfig=${CLUSTER_KUBECONFIG} get pods -A

You may also need to restart some deployments/daemonsets manually if they are stuck in an unhealthy state.