Rok 1.3 (unreleased)

This guide describes the necessary steps to upgrade an existing Rok cluster on Kubernetes from version 1.2 to the latest pre-release version, 1.3-rc8.

Check Kubernetes Version

Rok 1.3 only supports Kubernetes version 1.17, 1.18 or 1.19. Follow the instructions bellow to verify the Kubernetes version for your cluster, before continuing with the upgrade.

  1. Check your cluster version by inspecting the value of Server Version in the following command:

    root@rok-tools:/# kubectl version --short
    Client Version: v1.18.19
    Server Version: v1.19.13-eks-8df270
    
  2. If your Server Version is v1.17.* or v1.18.* or v.1.19.* you may proceed with the upgrade. If not, please follow the upgrade your cluster guide to upgrade your cluster to Kubernetes 1.17, 1.18 or 1.19.

Upgrade your management environment

We assume that you have followed the Deploy Rok Components guide, and have successfully set up a full-fledged rok-tools management environment either in local Docker or in Kubernetes.

Before proceeding with the core upgrade steps you need to first upgrade your management environment, in order to use CLI tools and utilities, such as rok-deploy that are compatible with the Rok version you are upgrading to.

Important

When you upgrade your management environment all previous data (GitOps repository, files, user settings, etc.) are preserved either in a Docker volume or Kubernetes PVC, depending on your environment. This volume or PVC is mounted in the new rok-tools container so that old data is adopted.

For Kubernetes simply apply the latest rok-tools manifests:

$ kubectl apply -f <download_root>/rok-tools-eks.yaml

Note

In case you see the following error:

The StatefulSet "rok-tools" is invalid: spec: Forbidden: updates to
statefulset spec for fields other than 'replicas', 'template', and
'updateStrategy' are forbidden

make sure your first delete the existing rok-tools StatefulSet with:

root@rok-tools:/# kubectl delete sts rok-tools

and then re-apply.

For Docker first delete the old container:

root@rok-tools:/# docker stop <OLD_ROK_TOOLS_CONTAINER_ID>
root@rok-tools:/# docker rm <OLD_ROK_TOOLS_CONTAINER_ID>

and then create a new one with previous data and the new image:

root@rok-tools:/# docker run -ti \
>     --name rok-tools \
>     --hostname rok-tools \
>     -p 8080:8080 \
>     --entrypoint /bin/bash \
>     -v $(pwd)/rok-tools-data:/root \
>     -v /var/run/docker.sock:/var/run/docker.sock \
>     -w /root \
>     gcr.io/arrikto/rok-tools:release-1.3-l0-release-1.3-rc8

Upgrade manifests

We assume that you have followed the Deploy Rok Components guide, and have a local GitOps repo with Arrikto-provided manifests. Once Arrikto releases a new Rok version and pushes updated deployment manifests, you have to follow the standard GitOps workflow:

  1. Fetch latest upstream changes, pushed by Arrikto.
  2. Rebase local changes on top of the latest upstream ones and resolve conflicts, if any.
  3. Tweak manifests based on Arrikto-provided instructions, if necessary.
  4. Commit everything.
  5. Re-apply manifests.

When one initially deploys Rok on Kubernetes, either automatically using rok-deploy or manually, they end up with a deploy overlay in each Rok component or external service that is to be applied to Kubernetes. In the GitOps deployment repository, Arrikto provides manifests that include the deploy overlay in each Kustomize app/package as scaffold, so that users can quickly start and set their preferences.

As a result, fetch/rebase might lead to conflicts since both Arrikto and the end-user might modify the same files that are tracked by Git. In this scenario, the most common and obvious solution is to keep the user’s changes since they are the ones that reflect the existing deployment.

In case of breaking changes, e.g., parts of YAML documents that are absolutely necessary to perform the upgrade, or others that might be deprecated, Arrikto will inform users via version-specific upgrade nodes for all actions that need to be taken.

Note

It is the user’s responsibility to apply valid manifests and kustomizations after a rebase. In case of uncertainty do not hesitate to coordinate with Arrikto’s Tech Team for support.

We will use git to update local manifests. You are about to rebase your work on top of latest pre-release branch. To favor local changes upon conflicts, we will use the corresponding merge strategy option.

Important

Make sure you mirror the GitOps repo to a private remote to be able to recover it in case of failure.

To upgrade the manifests:

  1. Go to your GitOps repository, inside your rok-tools management environment:

    root@rok-tools:/# cd ~/ops/deployments
    
  2. Fetch latest upstream changes:

    root@rok-tools:~/ops/deployments# git fetch --all -p
    Fetching origin
    
  3. Ensure the release channel you are currently following is release-1.2:

    root@rok-tools:~/ops/deployments# git rev-parse --abbrev-ref --symbolic-full-name @{u}
    origin/release-1.2
    

    If you are following the release-1.3 release channel already, you can skip to step 5.

  4. Follow the Switch release channel section to update to the release-1.3 release channel. You can skip this step if you are already in the release-1.3 release channel.

  5. Rebase on top of the latest pre-release version:

    root@rok-tools:~/ops/deployments# git rebase -Xtheirs
    
    Troubleshooting
    CONFLICT (modify/delete)

    Rebasing your work may cause conflicts when you have modified a file that has been removed from the latest version of Arrikto manifests. In such a case the rebase process will fail with:

    CONFLICT (modify/delete): path/to/file deleted in origin/release-1.3 and modified in HEAD~X. Version HEAD~X of path/to/file left in tree.
    
    1. Delete those files:

      root@rok-tools:~/ops/deployments# git status --porcelain | \
      >     awk '{if ($1=="DU") print $2}' | \
      >     xargs git rm
      
    2. Continue the rebase process:

      root@rok-tools:~/ops/deployments# git rebase --continue
      

Drain rok-csi nodes

To ensure minimal disruption of Rok services, please follow the following instructions to drain Rok CSI nodes, and wait for any pending Rok CSI operations to complete, before performing the upgrade.

During the upgrade, any pending Rok tasks will be canceled, so it is advisable to run the following steps in a period of inactivity, e.g., when no pipelines or snapshot policies run. Since pausing/queuing everything is currently not an option, one can monitor Rok logs and wait until nothing has been logged for, let’s say, 30 secs:

root@rok-tools:/# kubectl -n rok logs -l app=rok-csi-controller -c csi-controller -f --tail=100

Note

Finding a period of inactivity is an ideal scenario, that depending on the deployment may not be feasible, e.g., when having tens of recurring pipelines running. In such a case the end-user will simply see some of them fail.

  1. Scale down the rok-operator StatefulSet:

    root@rok-tools:/# kubectl -n rok-system scale sts rok-operator --replicas=0
    
  2. Ensure rok-operator scaled down to zero:

    root@rok-tools:/# kubectl get sts rok-operator -n rok-system
    
  3. Scale down the rok-csi-controller StatefulSet:

    root@rok-tools:/# kubectl -n rok scale sts rok-csi-controller --replicas=0
    
  4. Ensure rok-csi-controller scaled down to zero:

    root@rok-tools:/# kubectl get sts rok-csi-controller -n rok
    
  5. Watch the rok-csi-node logs and ensure that all pending operations have finished, i.e., nothing has been logged for the last 30 secs:

    root@rok-tools:/# kubectl -n rok logs -l app=rok-csi-node -c csi-node -f --tail=100
    
  6. Continue with the Upgrade components section.

Upgrade components

We assume that you are already running a 1.2 Rok cluster on Kubernetes and that you also have access to the 1.3-rc8 kustomization tree you are upgrading to.

Since a Rok cluster on Kubernetes consists of multiple components, you need to upgrade each one of them. Throughout the guide, we will keep track of these components, as listed in the table below:

Component old new
RokCluster CR  
RokCluster CRD  
Rok Operator  
Rok Disk Manager  
Rok kmod  

During the upgrade, Rok Operator will remove all members from the cluster and add a dedicated one to perform the upgrade. The cluster will be scaled down to zero and a Kubernetes Job will run to upgrade the cluster config on etcd and run any needed migrations. Finally, the cluster will be scaled back up to its initial size.

1. Increase observability (optional)

To gain insight into the status of the cluster upgrade execute the following commands in a separate window:

  • For live cluster status:

    root@rok-tools:/# watch kubectl get rokcluster -n rok
    
  • For live cluster events:

    root@rok-tools:/# watch 'kubectl describe rokcluster -n rok rok | tail -n 20'
    

2. Inspect current version (optional)

Get current images and version from the RokCluster CR:

root@rok-tools:/# kubectl describe rokcluster rok -n rok
...
Spec:
  Images:
    Rok:      gcr.io/arrikto-deploy/roke:release-1.2-l0-release-1.2
    Rok CSI:  gcr.io/arrikto-deploy/rok-csi:release-1.2-l0-release-1.2
Status:
  Version:        release-1.2-l0-release-1.2

3. Upgrade Rok Disk Manager

Apply the latest Rok Disk Manager manifests:

root@rok-tools:/# rok-deploy --apply rok/rok-disk-manager/overlays/deploy
Component old new
RokCluster CR  
RokCluster CRD  
Rok Operator  
Rok Disk Manager  
Rok kmod  

4. Upgrade Rok kmod

Apply the latest Rok kmod manifests:

root@rok-tools:/# rok-deploy --apply rok/rok-kmod/overlays/deploy
Component old new
RokCluster CR  
RokCluster CRD  
Rok Operator  
Rok Disk Manager  
Rok kmod  

5. Upgrade Rok cluster

Apply the latest Rok cluster manifests:

root@rok-tools:/# rok-deploy --apply rok/rok-cluster/overlays/deploy
Component old new
RokCluster CR  
RokCluster CRD  
Rok Operator  
Rok Disk Manager  
Rok kmod  

6. Upgrade Rok Operator

Apply the latest Operator manifests:

root@rok-tools:/# rok-deploy --apply rok/rok-operator/overlays/deploy

Note

The above command also updates the RokCluster CRD

After the manifests have been applied, ensure Rok Operator has become ready by running the following command:

root@rok-tools:/# watch kubectl get pods -n rok-system -l app=rok-operator
Component old new
RokCluster CR  
RokCluster CRD  
Rok Operator  
Rok Disk Manager  
Rok kmod  

7. Verify successful upgrade for Rok

  1. Check the status of the cluster upgrade Job:

    root@rok-tools:/# kubectl get job -n rok rok-upgrade-release-1.3-l0-release-1.3-rc8
    
  2. Ensure that Rok is up and running after the upgrade Job finishes:

    root@rok-tools:/# kubectl get rokcluster -n rok rok
    
  3. Ensure all pods in the rok-system namespace are up-and-running:

    root@rok-tools:/# kubectl get pods -n rok-system
    
  4. Ensure all pods in the rok namespace are up-and-running:

    root@rok-tools:/# kubectl get pods -n rok
    

Upgrade Istio

Rok 1.3-rc8 uses Istio 1.9.6. To upgrade from Istio 1.9.5 follow the next steps:

  1. Verify that Istio is up-and-running. Check that field READY is 1/1 and field UP-TO-DATE is 1:

    root@rok-tools:~/ops/deployments# kubectl get deployments -n istio-system
    NAME                    READY   UP-TO-DATE   AVAILABLE   AGE
    cluster-local-gateway   1/1     1            1           1m
    istio-ingressgateway    1/1     1            1           1m
    istiod                  1/1     1            1           1m
    
  2. Apply the new Istio control plane:

    root@rok-tools:~/ops/deployments# rok-deploy --apply install/istio
    
    root@rok-tools:~/ops/deployments# rok-deploy --apply rok/rok-external-services/istio/istio-1-9/cluster-local-gateway/overlays/deploy
    
  3. Confirm that the knative-serving and kubeflow namespaces, as well as all of the kubeflow user namespaces (namespaces that start with kubeflow-) have Istio sidecar injection enabled. To do this, run the following command and confirm that these namespaces show up in the command’s output:

    root@rok-tools:~/ops/deployments# kubectl get ns -l istio-injection=enabled
    NAME                        STATUS   AGE
    knative-serving             Active   5d16h
    kubeflow                    Active   5d16h
    kubeflow-user               Active   5d16h
    ...
    
  4. Upgrade the Istio sidecars, by deleting all Pods in the namespaces you found above. Istio will inject the new version sidecar once the owning controllers recreate the deleted Pods:

    root@rok-tools:~/ops/deployments# kubectl get ns -l istio-injection=enabled --no-headers | \
    >     awk '{print $1}' | \
    >         xargs -n1 -I {} kubectl delete pod --all -n {}
    

Upgrade cert-manager

Rok 1.3-rc8 uses cert-manager 1.3.1. To upgrade from cert-manager 0.11.0 follow the next steps:

  1. Apply the new cert-manager manifests:

    root@rok-tools:~/ops/deployments# rok-deploy --apply rok/cert-manager/cert-manager/overlays/deploy --force --force-kinds Deployment
    
  2. Remove the deprecated resources left by the previous version of Cert Manager:

    root@rok-tools:~/ops/deployments# rok-kf-prune --app cert-manager
    
  3. Verify that cert-manager is up-and-running. Check that field READY is 1/1 for the corresponding deployments:

    root@rok-tools:~/ops/deployments# kubectl get deploy -n cert-manager
    NAME                      READY   UP-TO-DATE   AVAILABLE   AGE
    cert-manager              1/1     1            1           1m
    cert-manager-cainjector   1/1     1            1           1m
    cert-manager-webhook      1/1     1            1           1m
    

Upgrade external services to protect System Pods

Rok 1.3-rc8 modified the manifests of the Rok external services to protect critical System Pods from OOM kills, evictions and CPU starvation. To apply these changes:

  1. Apply the new manifests for the Rok external services:

    root@rok-tools:~/ops/deployments# rok-deploy --apply \
    > rok/rok-external-services/{etcd,postgresql,redis}/overlays/deploy
    
  2. Verify that Rok external services are up-and-running. Check that field READY is 1/1 for the corresponding resources:

    root@rok-tools:~/ops/deployments# kubectl get sts -n rok
    NAME             READY   AGE
    rok-etcd         1/1     1m
    rok-postgresql   1/1     1m
    rok-redis        1/1     1m
    
  3. Apply the new manifests for the Dex/authservice external services:

    Warning

    Skip this step if you have deployed Kubeflow in your cluster.

    root@rok-tools:~/ops/deployments# rok-deploy --apply \
    > rok/rok-external-services/{dex,authservice}/overlays/deploy
    
  4. Verify that the Dex/authservice external services are up-and-running. Check that field READY is 1/1 for the corresponding resources:

    Warning

    Skip this step if you have deployed Kubeflow in your cluster.

    root@rok-tools:~/ops/deployments# kubectl get sts -n istio-system authservice
    NAME             READY   AVAILABLE   AGE
    authservice      1/1     1           1m
    
    root@rok-tools:~/ops/deployments# kubectl get deploy -n auth
    NAME   READY   UP-TO-DATE   AVAILABLE   AGE
    dex    1/1     1            1           1m
    
  5. (Azure only) Apply the new manifests for S3Proxy:

    root@rok-tools:~/ops/deployments# rok-deploy --apply \
    > rok/rok-external-services/s3proxy/overlays/deploy
    
  6. (Azure only) Verify that the S3 Proxy is up-and-running. Check that field READY is n, where n is the number of nodes in your cluster:

    root@rok-tools:~/ops/deployments# kubectl get ds -n rok rok-s3proxy
    NAME               DESIRED   CURRENT   READY   UP-TO-DATE   AVAILABLE     NODE SELECTOR   AGE
    rok-s3proxy        3         3         3       3            3             <none>          1m
    
  7. Apply the new manifests for the NGINX Ingress Controller:

    Note

    If you haven’t deployed the NGINX Ingress Controller, you may proceed to the Upgrade Kubeflow manifests section.

    root@rok-tools:~/ops/deployments# rok-deploy --apply \
    > rok/nginx-ingress-controller/overlays/deploy
    
  8. Verify that the NGINX Ingress Controller is up-and-running. Check that field READY is 1/1 for the corresponding resources:

    root@rok-tools:~/ops/deployments# kubectl get deploy -n ingress-nginx
    NAME                       READY   UP-TO-DATE   AVAILABLE   AGE
    nginx-ingress-controller   1/1     1            1           1m
    

Upgrade Kubeflow manifests

This section describes how to upgrade Kubeflow. If you have not deployed Kubeflow in your cluster, you can safely skip this section.

Run the following command to update your Kubeflow installation:

root@rok-tools:~/ops/deployments# rok-deploy --apply install/kubeflow

Upgrade Notebooks for EKF 1.3

  1. Modify all Notebooks that are using the deprecated kale-hp-tuning-image PodDefault, and upgrade them to the latest kale-python-image one, which uses a global Python image as a shim for Kale:

    root@rok-tools:~/ops/deployments# rok-notebook-upgrade \
    >    --label-selector kale-hp-tuning-image=true \
    >    --image gcr.io/arrikto/jupyter-kale-py36:release-1.3-l0-release-1.3-rc3-2-gadb3c0c1a \
    >    --remove-pod-default kale-hp-tuning-image \
    >    --add-pod-default kale-python-image
    
  2. Delete the deprecated PodDefault from all namespaces:

    root@rok-tools:/ops/deployments# NAMESPACES=$(ls kubeflow/manifests/common/namespace-resources/overlays)
    root@rok-tools:/ops/deployments# for ns in $NAMESPACES; do \
    >    kubectl -n $ns delete poddefaults.kubeflow.org kale-hp-tuning-image; \
    >    done
    

Upgrade JWA configuration

Update the Jupyter Web App configuration to use the new kale-python-image PodDefault instead of kale-hp-tuning-image, which has been removed.

Warning

Skip this section if you haven’t previously enabled the kale-hp-tuning-image PodDefault.

  1. Edit kubeflow/manifests/apps/jupyter/jupyter-web-app/upstream/overlays/deploy/patches/config-map.yaml and update the configurations list and replace the deprecated kale-hp-tuning-image label with the kale-python-image one.

    configurations:
      value:
        - access-rok
        - access-ml-pipeline
        - kale-hp-tuning-image  # <-- Remove this line
        - kale-python-image  # <-- Add this line
    

    The final result should look like this:

    configurations:
      value:
        - access-rok
        - access-ml-pipeline
        - kale-python-image
    
  2. Commit changes:

    root@rok-tools:~/ops/deployments# git commit -am "Update enabled JWA PodDefaults"
    
  3. Apply changes:

    root@rok-tools:~/ops/deployments# rok-deploy --apply \
    >     kubeflow/manifests/apps/jupyter/jupyter-web-app/upstream/overlays/deploy
    

Delete stale Kubeflow resources

Run the following command to remove the deprecated resources left by the previous version of Kubeflow:

root@rok-tools:~/ops/deployments# rok-kf-prune --app kubeflow

Verify successful upgrade

Follow the Verify section to validate the updated Rok + EKF deployment.