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Upgrade Kubernetes cluster on AWS

Upgrade Kubernetes cluster on AWS#

Warning

This upgrade will cause disruptions for users and trigger alerts for Simple HTTPS uptime checks. To help other engineers, communicate that your are starting a cluster upgrade in the #maintenance-notices Slack channel and setup a snooze

Warning

We haven’t yet established a policy for planning and communicating maintenance procedures to users. So preliminary, only make a k8s cluster upgrade while the cluster is unused or that the maintenance is communicated ahead of time.

Pre-requisites#

  1. Install or upgrade CLI tools

    Install required tools as documented in Prerequisites, and ensure you have a recent version of eksctl.

    Warning

    Using a modern version of eksctl has been found important historically, make sure to use the latest version to avoid debugging an already fixed bug!

  2. Consider changes to template.jsonnet

    The eksctl config jinja2 template eksctl/template.jsonnet was once used to generate the jsonnet template eksctl/$CLUSTER_NAME.jsonnet, that has been used to generate an actual eksctl config.

    Before upgrading an EKS cluster, it could be a good time to consider changes to eksctl/template.jsonnet since this cluster’s jsonnet template was last generated, which it was initially according to Generate cluster files.

    To do this first ensure git status reports no changes, then generate new cluster files using the deployer script, then restore changes to everything but the eksctl/$CLUSTER_NAME.jsonnet file.

    export CLUSTER_NAME=<cluster-name>
export CLUSTER_REGION=<cluster-region-like ca-central-1>
export HUB_TYPE=<hub-type-like-basehub>

    # only continue below if git status reports a clean state
git status

# generates a few new files
deployer generate dedicated-cluster aws --cluster-name=$CLUSTER_NAME --cluster-region=$CLUSTER_REGION --hub-type=$HUB_TYPE

# overview changed files
git status

# restore changes to all files but the .jsonnet files
git add *.jsonnet
git checkout ..  # .. should be the git repo's root
git reset

# inspect changes
git diff

    Finally if you identify changes you think should be retained, add and commit them. Discard the remaining changes with a git checkout . command.

  3. Learn how to generate an eksctl config file

    When upgrading an EKS cluster, we will use eksctl extensively and reference a generated config file, $CLUSTER_NAME.eksctl.yaml. It’s generated from the the $CLUSTER_NAME.jsonnet file.

    # re-generate an eksctl config file for use with eksctl
jsonnet $CLUSTER_NAME.jsonnet > $CLUSTER_NAME.eksctl.yaml

    Important

    If you update the .jsonnet file, make sure to re-generate the .yaml file before using eksctl.

    Respectively if you update the .yaml file directly, remember to update the .jsonnet file.

Cluster upgrade#

1. Ensure in-cluster permissions#

The k8s api-server won’t accept commands from you unless you have configured a mapping between the AWS user to a k8s user, and eksctl needs to make some commands behind the scenes.

This mapping is done from a ConfigMap in kube-system called aws-auth, and we can use an eksctl command to influence it.

eksctl create iamidentitymapping \
   --cluster=$CLUSTER_NAME \
   --region=$CLUSTER_REGION \
   --arn=arn:aws:iam::<aws-account-id>:user/<iam-user-name> \
   --username=<iam-user-name> \
   --group=system:masters

2. Acquire and configure AWS credentials#

Visit https://2i2c.awsapps.com/start#/ and acquire CLI credentials.

In case the AWS account isn’t managed there, inspect config/$CLUSTER_NAME/cluster.yaml to understand what AWS account number to login to at https://console.aws.amazon.com/.

Configure credentials like:

export AWS_ACCESS_KEY_ID="..."
export AWS_SECRET_ACCESS_KEY="..."

3. Upgrade the k8s control plane one minor version#

Important

The k8s control plane can only be upgraded one minor version at the time.[1]

3.1. Update the cluster’s version field one minor version.#

In the cluster’s config file there should be an entry like the one below, where the version must be updated.

{
   name: "openscapeshub",
   region: clusterRegion,
   version: '1.27'
}

Then, perform the upgrade which typically takes ~10 minutes.

eksctl upgrade cluster --config-file=$CLUSTER_NAME.eksctl.yaml --approve

Note

If you see the error Error: the server has asked for the client to provide credentials don’t worry, if you try it again you will find that the cluster is now upgraded.

3.2. Upgrade EKS add-ons#

As documented in eksctl’s documentation[1], we also need to upgrade three EKS add-ons enabled by default, and one we have added manually.

# upgrade the kube-proxy daemonset (takes ~5s)
eksctl utils update-kube-proxy --config-file=$CLUSTER_NAME.eksctl.yaml --approve

# upgrade the aws-node daemonset (takes ~5s)
eksctl utils update-aws-node --config-file=$CLUSTER_NAME.eksctl.yaml --approve

# upgrade the coredns deployment (takes ~5s)
eksctl utils update-coredns --config-file=$CLUSTER_NAME.eksctl.yaml --approve

# upgrade the aws-ebs-csi-driver addon's deployment and daemonset (takes ~60s)
eksctl update addon --config-file=$CLUSTER_NAME.eksctl.yaml

Note

Common failures The kube-proxy deamonset’s pods may fail to pull the image, to resolve this visit AWS EKS docs on managing coredns to identify the version to use and update the coredns deployment’s container image to match it.

kubectl edit daemonset coredns -n kube-system

4. Repeat step 3 above for up to three times, if needed#

If you upgrade k8s multiple minor versions, consider repeating step 3, up to maximum three times, incrementing the control plane one minor version at the time.

This is because the control plane version can be ahead of the node’s k8s software (kubelet) by up to three minor versions [2] if kublet is at least at version 1.25. Due to this, you can plan your cluster upgrade to only involve the minimum number of node group upgrades.

So if you upgrade from k8s 1.25 to 1.28, you can for example upgrade the k8s control plane three steps in a row, from 1.25 to 1.26, then from 1.26 to 1.27 and then from 1.27 to 1.28. This way, the node groups were left behind the control plane by three minor versions, which is ok, because it doesn’t break the three minor versions rule.

Then, you can upgrade the node groups directly from 1.25 to 1.28 making only one upgrade on the node groups instead of three.

5. Upgrade node groups version until it matches the k8s control plane#

Important

Per step 4 above, you can upgrade the version of the node groups maximum three versions at once, for example from 1.25 to 1.28 directly if the control plane’s version allows it.

If after one such upgrade, the node groups version is still behind the k8s control plane, you will need to repeat the node upgrade process until it does.

To upgrade (unmanaged) node groups, you delete them and then add them back in. When adding them back, make sure your cluster config’s k8s version is what you want the node groups to be added back as.

5.1. Double-check current k8s version in the config#

Up until this step, you should have updated the control plane’s version at least once but for maximum of three times. So you shouldn’t need to update it.

However, it is worth double checking that the k8s version that is in the config file is:

  • not ahead of the current k8s control plane version, as this will influence the version of the node groups.

  • not more than three minor versions than what the version of node groups was initially

5.2. Renaming node groups part 1: add a new core node group (like core-b)#

Rename the config file’s entry for the core node group temporarily when running this command, either from core-a to core-b or the other way around, then create the new nodegroup.

# create a copy of the current nodegroup (takes ~5 min)
eksctl create nodegroup --config-file=$CLUSTER_NAME.eksctl.yaml --include="core-b"

Important

The eksctl create nodegroup can fail quietly when re-creating a node group that has been deleted recently (last ~60 seconds). If you see messages like # existing nodegroup(s) (…) will be excluded and created 0 nodegroup(s), you can just re-run the create command.

5.3. Renaming node groups part 2: delete all old node groups (like core-a,nb-*,dask-*)#

Rename the core node group again in the config to its previous name, so the old node group can be deleted with the following command, then delete the original nodegroup.

# delete the original nodegroup (takes ~20s if the node groups has no running nodes)
eksctl delete nodegroup --config-file=$CLUSTER_NAME.eksctl.yaml --include="core-a,nb-*,dask-*" --approve --drain=true

Note

The eksctl managed drain operation may get stuck but you could help it along by finding the pods that fail to terminate with kubectl get pod -A, and then manually forcefully terminating them with kubectl delete pod --force <...>.

5.4. Renaming node groups part 3: re-create all non-core node groups (like nb-*,dask-*)#

Rename the core node group one final time in the config to its new name, as that represents the state of the EKS cluster.

eksctl create nodegroup --config-file=$CLUSTER_NAME.eksctl.yaml --include="nb-*,dask-*"

6. Repeat steps 3,4,5 if needed#

If you need to upgrade the cluster more than three minor versions, consider repeating steps 3, 4 and 5 until the desired version is reached.

7. Commit the changes to the jsonnet config file#

During this upgrade, the k8s version and possibly the node group name might have been changed. Make sure you commit this changes after the upgrade is finished.

References#

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