Remove a storage node

Steps to remove a storage node of an OpenShift 4 cluster on Exoscale.

Starting situation

  • You already have a OpenShift 4 cluster on Exoscale

  • You have admin-level access to the cluster

  • You want to remove an existing storage node in the cluster

Prerequisites

The following CLI utilities need to be available locally:

Prepare local environment

  1. Create local directory to work in

    We strongly recommend creating an empty directory, unless you already have a work directory for the cluster you’re about to work on. This guide will run Commodore in the directory created in this step.

    export WORK_DIR=/path/to/work/dir
    mkdir -p "${WORK_DIR}"
    pushd "${WORK_DIR}"
  2. Configure API access

    Access to cloud API
    export EXOSCALE_API_KEY=<exoscale-key>
    export EXOSCALE_API_SECRET=<exoscale-secret>
    export EXOSCALE_ZONE=<exoscale-zone> (1)
    export EXOSCALE_S3_ENDPOINT="sos-${EXOSCALE_ZONE}.exo.io"
    1 All lower case. For example ch-dk-2.
    Access to various API
    # From https://git.vshn.net/-/profile/personal_access_tokens, "api" scope is sufficient
    export GITLAB_TOKEN=<gitlab-api-token>
    export GITLAB_USER=<gitlab-user-name>
    
    # For example: https://api.syn.vshn.net
    # IMPORTANT: do NOT add a trailing `/`. Commands below will fail.
    export COMMODORE_API_URL=<lieutenant-api-endpoint>
    export COMMODORE_API_TOKEN=<lieutenant-api-token>
    
    # Set Project Syn cluster and tenant ID
    export CLUSTER_ID=<lieutenant-cluster-id> # Looks like: c-<something>
    export TENANT_ID=$(curl -sH "Authorization: Bearer ${COMMODORE_API_TOKEN}" ${COMMODORE_API_URL}/clusters/${CLUSTER_ID} | jq -r .tenant)
  3. Get required tokens from Vault

    Connect with Vault
    export VAULT_ADDR=https://vault-prod.syn.vshn.net
    vault login -method=ldap username=<your.name>
    Grab the LB hieradata repo token from Vault
    export HIERADATA_REPO_SECRET=$(vault kv get \
      -format=json "clusters/kv/lbaas/hieradata_repo_token" | jq '.data.data')
    export HIERADATA_REPO_USER=$(echo "${HIERADATA_REPO_SECRET}" | jq -r '.user')
    export HIERADATA_REPO_TOKEN=$(echo "${HIERADATA_REPO_SECRET}" | jq -r '.token')
    Get Floaty credentials
    export TF_VAR_lb_exoscale_api_user=$(vault kv get \
      -format=json "clusters/kv/${TENANT_ID}/${CLUSTER_ID}/floaty" | jq '.data.data')
    export TF_VAR_lb_exoscale_api_key=$(echo "${TF_VAR_lb_exoscale_api_user}" | jq -r '.iam_key')
    export TF_VAR_lb_exoscale_api_secret=$(echo "${TF_VAR_lb_exoscale_api_user}" | jq -r '.iam_secret')
  4. Compile the catalog for the cluster. Having the catalog available locally enables us to run Terraform for the cluster to make any required changes.

    commodore catalog compile "${CLUSTER_ID}"

Set alert silence

  1. Set a silence in Alertmanager for all rook-ceph alerts

    if [[ "$OSTYPE" == "darwin"* ]]; then alias date=gdate; fi
    job_name=$(printf "POST-silence-rook-ceph-alerts-$(date +%s)" | tr '[:upper:]' '[:lower:]')
    silence_duration='+60 minutes' (1)
    kubectl --as=cluster-admin -n openshift-monitoring create -f- <<EOJ
    apiVersion: batch/v1
    kind: Job
    metadata:
      name: ${job_name}
      labels:
        app: silence-rook-ceph-alerts
    spec:
     backoffLimit: 0
     template:
      spec:
        restartPolicy: Never
        containers:
          - name: silence
            image: quay.io/appuio/oc:v4.6
            command:
            - bash
            - -c
            - |
              curl_opts=( --cacert /etc/ssl/certs/serving-certs/service-ca.crt --header "Content-Type: application/json" --header "Authorization: Bearer \$(cat /var/run/secrets/kubernetes.io/serviceaccount/token)" --resolve alertmanager-main.openshift-monitoring.svc.cluster.local:9095:\$(getent hosts alertmanager-operated.openshift-monitoring.svc.cluster.local | awk '{print \$1}' | head -n 1) --silent )
              read -d "" body << EOF
              {
                "matchers": [
                  {
                    "name": "syn_component",
                    "value": "rook-ceph",
                    "isRegex": false
                  }
                ],
                "startsAt": "$(date -u +'%Y-%m-%dT%H:%M:%S')",
                "endsAt": "$(date -u +'%Y-%m-%dT%H:%M:%S' --date "${silence_duration}")",
                "createdBy": "$(kubectl config current-context | cut -d/ -f3)",
                "comment": "Silence all rook-ceph alerts"
              }
              EOF
    
              curl "\${curl_opts[@]}" \
                "https://alertmanager-main.openshift-monitoring.svc.cluster.local:9095/api/v2/silences" \
                -XPOST -d "\${body}"
    
            volumeMounts:
            - mountPath: /etc/ssl/certs/serving-certs/
              name: ca-bundle
              readOnly: true
        serviceAccountName: prometheus-k8s
        volumes:
        - name: ca-bundle
          configMap:
            defaultMode: 288
            name: serving-certs-ca-bundle
    EOJ
    1 Adjust this variable to create a longer or shorter silence
  2. Extract Alertmanager silence ID from job logs

    silence_id=$(kubectl --as=cluster-admin -n openshift-monitoring logs jobs/${job_name} | \
      jq -r '.silenceID')

Update Cluster Config

  1. Update cluster config.

    pushd "inventory/classes/${TENANT_ID}/"
    
    yq eval -i ".parameters.openshift4_terraform.terraform_variables.storage_count -= 1" \
      ${CLUSTER_ID}.yml
    
    yq eval -i ".parameters.rook_ceph.ceph_cluster.node_count -= 1" \
      ${CLUSTER_ID}.yml

    Ceph can’t scale to less than 3 storage nodes, which is the default number of nodes. Please ensure that this update doesn’t reduce the number of storage nodes to less than 3 before continuing.

  2. Review and commit

    # Have a look at the file ${CLUSTER_ID}.yml.
    
    git commit -a -m "Remove storage node from cluster ${CLUSTER_ID}"
    git push
    
    popd
  3. Compile and push cluster catalog

    commodore catalog compile ${CLUSTER_ID} --push -i

Prepare Terraform environment

  1. Configure Terraform secrets

    cat <<EOF > ./terraform.env
    EXOSCALE_API_KEY
    EXOSCALE_API_SECRET
    TF_VAR_lb_exoscale_api_key
    TF_VAR_lb_exoscale_api_secret
    TF_VAR_control_vshn_net_token
    GIT_AUTHOR_NAME
    GIT_AUTHOR_EMAIL
    HIERADATA_REPO_TOKEN
    EOF
  2. Setup Terraform

    Prepare Terraform execution environment
    # Set terraform image and tag to be used
    tf_image=$(\
      yq eval ".parameters.openshift4_terraform.images.terraform.image" \
      dependencies/openshift4-terraform/class/defaults.yml)
    tf_tag=$(\
      yq eval ".parameters.openshift4_terraform.images.terraform.tag" \
      dependencies/openshift4-terraform/class/defaults.yml)
    
    # Generate the terraform alias
    base_dir=$(pwd)
    alias terraform='docker run -it --rm \
      -e REAL_UID=$(id -u) \
      --env-file ${base_dir}/terraform.env \
      -w /tf \
      -v $(pwd):/tf \
      --ulimit memlock=-1 \
      "${tf_image}:${tf_tag}" /tf/terraform.sh'
    
    export GITLAB_REPOSITORY_URL=$(curl -sH "Authorization: Bearer ${COMMODORE_API_TOKEN}" ${COMMODORE_API_URL}/clusters/${CLUSTER_ID} | jq -r '.gitRepo.url' | sed 's|ssh://||; s|/|:|')
    export GITLAB_REPOSITORY_NAME=${GITLAB_REPOSITORY_URL##*/}
    export GITLAB_CATALOG_PROJECT_ID=$(curl -sH "Authorization: Bearer ${GITLAB_TOKEN}" "https://git.vshn.net/api/v4/projects?simple=true&search=${GITLAB_REPOSITORY_NAME/.git}" | jq -r ".[] | select(.ssh_url_to_repo == \"${GITLAB_REPOSITORY_URL}\") | .id")
    export GITLAB_STATE_URL="https://git.vshn.net/api/v4/projects/${GITLAB_CATALOG_PROJECT_ID}/terraform/state/cluster"
    
    pushd catalog/manifests/openshift4-terraform/
    Initialize Terraform
    terraform init \
      "-backend-config=address=${GITLAB_STATE_URL}" \
      "-backend-config=lock_address=${GITLAB_STATE_URL}/lock" \
      "-backend-config=unlock_address=${GITLAB_STATE_URL}/lock" \
      "-backend-config=username=${GITLAB_USER}" \
      "-backend-config=password=${GITLAB_TOKEN}" \
      "-backend-config=lock_method=POST" \
      "-backend-config=unlock_method=DELETE" \
      "-backend-config=retry_wait_min=5"

Remove Node

  • Find the node you want to remove. It has to be the one with the highest terraform index.

    # Grab JSON copy of current Terraform state
    terraform state pull > .tfstate.json
    
    node_count=$(jq  -r \
      '.resources[] |
       select(.module=="module.cluster.module.storage" and .type=="exoscale_compute") |
       .instances | length' \
       .tfstate.json)
    # Verify that the number of nodes is one more than we configured earlier.
    echo $node_count
    
    export NODE_TO_REMOVE=$(jq --arg index "$node_count" -r \
      '.resources[] |
       select(.module=="module.cluster.module.storage" and .type=="exoscale_compute") |
       .instances[$index|tonumber-1] |
       .attributes.hostname' \
       .tfstate.json)
    echo $NODE_TO_REMOVE

Remove old OSD

  1. Make sure ArgoCD ran and reduced the target number of OSDs

    kubectl --as=cluster-admin -n syn-rook-ceph-cluster \
      get cephcluster cluster -o jsonpath='{.spec.storage.storageClassDeviceSets[0].count}'
  2. Disable ArgoCD auto sync for component rook-ceph

    kubectl --as=cluster-admin -n syn patch apps root --type=json \
      -p '[{"op":"replace", "path":"/spec/syncPolicy", "value": {}}]'
    kubectl --as=cluster-admin -n syn patch apps rook-ceph --type=json \
      -p '[{"op":"replace", "path":"/spec/syncPolicy", "value": {}}]'
  3. Scale down the Rook-Ceph operator

    kubectl --as=cluster-admin -n syn-rook-ceph-operator scale --replicas=0 \
      deploy/rook-ceph-operator
  4. Tell Ceph to take the OSD(s) on the node(s) to remove out of service and relocate data stored on them

    # Verify that the list of nodes to replace is correct
    echo $NODE_TO_REMOVE
    # Reweight OSDs on those nodes to 0
    for node in $(echo -n $NODE_TO_REMOVE); do
      osd_id=$(kubectl --as=cluster-admin -n syn-rook-ceph-cluster get deploy \
        -l failure-domain="${node}" --no-headers \
        -o custom-columns="OSD_ID:.metadata.labels.ceph_daemon_id")
      kubectl --as=cluster-admin -n syn-rook-ceph-cluster exec -it deploy/rook-ceph-tools -- \
        ceph osd crush reweight "osd.${osd_id}" 0
    done
  5. Wait for the data to be redistributed ("backfilled")

    When backfilling is completed, ceph status should show all PGs as active+clean.
    Depending on the number of OSDs in the storage cluster and the amount of data that needs to be moved, this may take a while.

    If the storage cluster is mostly idle, you can speed up backfilling by temporarily setting the following configuration.

    kubectl --as=cluster-admin -n syn-rook-ceph-cluster exec -it deploy/rook-ceph-tools -- \
      ceph config set osd osd_max_backfills 10 (1)
    1 The number of PGs which are allowed to backfill in parallel. Adjust up or down depending on client load on the storage cluster.

    After backfilling is completed, you can remove the configuration with

    kubectl --as=cluster-admin -n syn-rook-ceph-cluster exec -it deploy/rook-ceph-tools -- \
      ceph config rm osd osd_max_backfills
    kubectl --as=cluster-admin -n syn-rook-ceph-cluster exec -it deploy/rook-ceph-tools -- \
      ceph status
  6. Remove the OSD(s) from the Ceph cluster

    for node in $(echo -n $NODE_TO_REMOVE); do
      osd_id=$(kubectl --as=cluster-admin -n syn-rook-ceph-cluster get deploy \
        -l failure-domain="${node}" --no-headers \
        -o custom-columns="OSD_ID:.metadata.labels.ceph_daemon_id")
      kubectl --as=cluster-admin -n syn-rook-ceph-cluster exec -it deploy/rook-ceph-tools -- \
        ceph osd out "${osd_id}"
      kubectl --as=cluster-admin -n syn-rook-ceph-cluster scale --replicas=0 \
        "deploy/rook-ceph-osd-${osd_id}"
      kubectl --as=cluster-admin -n syn-rook-ceph-cluster exec -it deploy/rook-ceph-tools -- \
        ceph osd purge "${osd_id}"
      kubectl --as=cluster-admin -n syn-rook-ceph-cluster exec -it deploy/rook-ceph-tools -- \
        ceph osd crush remove "${node}"
    done
  7. Check that the OSD is no longer listed in ceph osd tree

    kubectl --as=cluster-admin -n syn-rook-ceph-cluster exec -it deploy/rook-ceph-tools -- \
      ceph osd tree
  8. Make a note of the PVC(s) of the old OSD(s)

    We also extract the name of the PV(s) here, but we’ll only delete the PV(s) after removing the node(s) from the cluster.
    old_pvc_names=""
    old_pv_names=""
    for node in $(echo -n $NODE_TO_REMOVE); do
      osd_id=$(kubectl --as=cluster-admin -n syn-rook-ceph-cluster get deploy \
        -l failure-domain="${node}" --no-headers \
        -o custom-columns="NAME:.metadata.name" | cut -d- -f4)
    
      pvc_name=$(kubectl --as=cluster-admin -n syn-rook-ceph-cluster get deploy \
        "rook-ceph-osd-${osd_id}" -ojsonpath='{.metadata.labels.ceph\.rook\.io/pvc}')
      pv_name=$(kubectl --as=cluster-admin -n syn-rook-ceph-cluster get pvc \
        "${pvc_name}" -o jsonpath='{.spec.volumeName}')
    
      old_pvc_names="$old_pvc_names $pvc_name"
      old_pv_names="$old_pv_names $pv_name"
    done
    echo $old_pvc_names
    echo $old_pv_names
  9. Delete old OSD deployment(s)

    for node in $(echo -n $NODE_TO_REMOVE); do
      kubectl --as=cluster-admin -n syn-rook-ceph-cluster delete deploy \
        -l failure-domain="${node}"
    done
  10. Clean up PVC(s) and prepare job(s) of the old OSD(s) if necessary

    for pvc_name in $(echo -n $old_pvc_names); do
      kubectl --as=cluster-admin -n syn-rook-ceph-cluster delete job \
        -l ceph.rook.io/pvc="${pvc_name}"
      kubectl --as=cluster-admin -n syn-rook-ceph-cluster delete pvc "${pvc_name}"
    done
  11. Clean up PVC encryption secret(s)

    for pvc_name in $(echo -n $old_pvc_names); do
      kubectl --as=cluster-admin -n syn-rook-ceph-cluster delete secret -l pvc_name="${pvc_name}"
    done
  12. Scale up the Rook-Ceph operator

    kubectl --as=cluster-admin -n syn-rook-ceph-operator scale --replicas=1 \
      deploy/rook-ceph-operator

Remove the old MON

  1. Find the MON(s) (if any) on the node(s) to remove

    MON_IDS=""
    for node in $(echo -n $NODE_TO_REMOVE); do
      mon_id=$(kubectl --as=cluster-admin -n syn-rook-ceph-cluster get pods \
        -lapp=rook-ceph-mon --field-selector="spec.nodeName=${node}" \
        --no-headers -ocustom-columns="MON_ID:.metadata.labels.ceph_daemon_id")
      MON_IDS="$MON_IDS $mon_id"
    done
    echo $MON_IDS
    You can skip the remaining steps in this section if $MON_ID is empty.
  2. Temporarily adjust the Rook MON failover timeout. This tells the operator to perform the MON failover after less time than the default 10 minutes.

    kubectl --as=cluster-admin -n syn-rook-ceph-cluster patch cephcluster cluster --type=json \
      -p '[{
        "op": "replace",
        "path": "/spec/healthCheck/daemonHealth/mon",
        "value": {
          "disabled": false,
          "interval": "10s",
          "timeout": "10s"
        }
      }]'
  3. Cordon node(s) to remove

    for node in $(echo -n $NODE_TO_REMOVE); do
      kubectl --as=cluster-admin cordon "${node}"
    done
  4. For every id in $MON_IDS replace the MON pod

    mon_id=<MON_ID>
    kubectl --as=cluster-admin -n syn-rook-ceph-cluster delete pod \
      -l app=rook-ceph-mon,ceph_daemon_id="${mon_id}"
    
    # Wait until new MON is scheduled
    kubectl --as=cluster-admin -n syn-rook-ceph-cluster get pods -w
    
    # Wait until the cluster has regained full quorum
    kubectl --as=cluster-admin -n syn-rook-ceph-cluster exec -it deploy/rook-ceph-tools -- \
      ceph status
    
    # Repeat for all other $MON_IDS
  5. Verify that three MONs are running

    kubectl --as=cluster-admin -n syn-rook-ceph-cluster get deploy -l app=rook-ceph-mon
  6. Reset the MON failover timeout

    kubectl --as=cluster-admin -n syn-rook-ceph-cluster patch cephcluster cluster --type=json \
      -p '[{
        "op": "replace",
        "path": "/spec/healthCheck/daemonHealth/mon",
        "value": {}
      }]'

Remove VM

  1. Drain the node(s) to replace

    for node in $(echo -n ${NODE_TO_REMOVE}); do
      kubectl --as=cluster-admin drain "${node}" \
        --delete-emptydir-data --ignore-daemonsets
    done
  2. Delete the node(s) to replace from the cluster

    for node in $(echo -n ${NODE_TO_REMOVE}); do
      kubectl --as=cluster-admin delete node "${node}"
    done
  3. Remove the node(s) by applying Terraform

    Verify that the hostname of the to be deleted node(s) matches ${NODE_TO_REMOVE}

    Ensure that you’re still in directory ${WORK_DIR}/catalog/manifests/openshift4-terraform before executing this command.
    terraform apply

Finish up

  1. Remove silence in Alertmanager

    if [[ "$OSTYPE" == "darwin"* ]]; then alias date=gdate; fi
    job_name=$(printf "DELETE-silence-rook-ceph-alerts-$(date +%s)" | tr '[:upper:]' '[:lower:]')
    kubectl --as=cluster-admin -n openshift-monitoring create -f- <<EOJ
    apiVersion: batch/v1
    kind: Job
    metadata:
      name: ${job_name}
      labels:
        app: silence-rook-ceph-alerts
    spec:
     backoffLimit: 0
     template:
      spec:
        restartPolicy: Never
        containers:
          - name: silence
            image: quay.io/appuio/oc:v4.6
            command:
            - bash
            - -c
            - |
              curl_opts=( --cacert /etc/ssl/certs/serving-certs/service-ca.crt --header "Content-Type: application/json" --header "Authorization: Bearer \$(cat /var/run/secrets/kubernetes.io/serviceaccount/token)" --resolve alertmanager-main.openshift-monitoring.svc.cluster.local:9095:\$(getent hosts alertmanager-operated.openshift-monitoring.svc.cluster.local | awk '{print \$1}' | head -n 1) --silent )
    
              curl "\${curl_opts[@]}" \
                "https://alertmanager-main.openshift-monitoring.svc.cluster.local:9095/api/v2/silence/${silence_id}" \
                -XDELETE
    
            volumeMounts:
            - mountPath: /etc/ssl/certs/serving-certs/
              name: ca-bundle
              readOnly: true
        serviceAccountName: prometheus-k8s
        volumes:
        - name: ca-bundle
          configMap:
            defaultMode: 288
            name: serving-certs-ca-bundle
    EOJ
  2. Clean up Alertmanager silence jobs

    kubectl --as=cluster-admin -n openshift-monitoring delete jobs -l app=silence-rook-ceph-alerts
  3. Re-enable ArgoCD auto sync

    kubectl --as=cluster-admin -n syn patch apps root --type=json \
      -p '[{
        "op":"replace",
        "path":"/spec/syncPolicy",
        "value": {"automated": {"prune": true, "selfHeal": true}}
      }]'

Upstream documentation