Managing Persistent Volumes

Some of the included services require persistent storage, configured through Persistent Volumes that specify which disks your cluster has access to. Documentation on the storage configuration necessary to install this chart can be found in our Storage Guide

Storage changes after installation need to be manually handled by your cluster administrators. Automated management of these volumes after installation is not handled by the GitLab chart.

Examples of changes not automatically managed after initial installation include:

  • Mounting different volumes to the Pods
  • Changing the effective accessModes or Storage Class
  • Expanding the storage size of your volume*1

1 In Kubernetes 1.11, expanding the storage size of your volume is supported if you have allowVolumeExpansion configured to true in your Storage Class.

Automating theses changes is complicated due to:

  1. Kubernetes does not allow changes to most fields in an existing PersistentVolumeClaim
  2. Unless manually configured, the PVC is the only reference to dynamically provisioned PersistentVolumes
  3. Delete is the default reclaimPolicy for dynamically provisioned PersistentVolumes

This means in order to make changes, we need to delete the PersistentVolumeClaim and create a new one with our changes. But due to the default reclaimPolicy, deleting the PersistentVolumeClaim may delete the PersistentVolumes and underlying disk. And unless configured with appropriate volumeNames and/or labelSelectors, the chart won’t know the volume to attach to.

We will continue to look into making this process easier, but for now a manual process needs to be followed to make changes to your storage.

Locate the GitLab Volumes

Find the volumes/claims that are being used:

kubectl --namespace <namespace> get PersistentVolumeClaims -l release=<chart release name> -ojsonpath='{range .items[*]}{.spec.volumeName}{"\t"}{.metadata.labels.app}{"\n"}{end}'
  • <namespace> should be replaced with the namespace where you installed the GitLab chart.
  • <chart release name> should be replaced with the name you used to install the GitLab chart.

The command will print a list of the volume names, followed by the name of the service they are for.

For example:

$ kubectl --namespace helm-charts-win get PersistentVolumeClaims -l release=review-update-app-h8qogp -ojsonpath='{range .items[*]}{.spec.volumeName}{"\t"}{.metadata.labels.app}{"\n"}{end}'
pvc-6247502b-8c2d-11e8-8267-42010a9a0113	gitaly
pvc-61bbc05e-8c2d-11e8-8267-42010a9a0113	minio
pvc-61bc6069-8c2d-11e8-8267-42010a9a0113	postgresql
pvc-61bcd6d2-8c2d-11e8-8267-42010a9a0113	prometheus
pvc-61bdf136-8c2d-11e8-8267-42010a9a0113	redis

Before making storage changes

Note: The person making the changes needs to have admin access to the cluster, and appropriate access to the storage solutions being used. Often the changes will first need to be applied in the storage solution, then the results need to be updated in Kubernetes.

Before making changes, you should ensure your PersistentVolumes are using the Retain reclaimPolicy so they don’t get removed while you are making changes.

First, find the volumes/claims that are being used.

Next, edit each volume and change the value of persistentVolumeReclaimPolicy under the spec field, to be Retain rather than Delete

For example:

$ kubectl --namespace helm-charts-win edit PersistentVolume pvc-6247502b-8c2d-11e8-8267-42010a9a0113
Editing Output: 

  # Please edit the object below. Lines beginning with a '#' will be ignored,
  # and an empty file will abort the edit. If an error occurs while saving this file will be
  # reopened with the relevant failures.
  #
  apiVersion: v1
  kind: PersistentVolume
  metadata:
    annotations:
      kubernetes.io/createdby: gce-pd-dynamic-provisioner
      pv.kubernetes.io/bound-by-controller: "yes"
      pv.kubernetes.io/provisioned-by: kubernetes.io/gce-pd
    creationTimestamp: 2018-07-20T14:58:43Z
    labels:
      failure-domain.beta.kubernetes.io/region: europe-west2
      failure-domain.beta.kubernetes.io/zone: europe-west2-b
    name: pvc-6247502b-8c2d-11e8-8267-42010a9a0113
    resourceVersion: "48362431"
    selfLink: /api/v1/persistentvolumes/pvc-6247502b-8c2d-11e8-8267-42010a9a0113
    uid: 650bd649-8c2d-11e8-8267-42010a9a0113
  spec:
    accessModes:
    - ReadWriteOnce
    capacity:
      storage: 50Gi
    claimRef:
      apiVersion: v1
      kind: PersistentVolumeClaim
      name: repo-data-review-update-app-h8qogp-gitaly-0
      namespace: helm-charts-win
      resourceVersion: "48362307"
      uid: 6247502b-8c2d-11e8-8267-42010a9a0113
    gcePersistentDisk:
      fsType: ext4
      pdName: gke-cloud-native-81a17-pvc-6247502b-8c2d-11e8-8267-42010a9a0113
  # Changed the following line
    persistentVolumeReclaimPolicy: Retain
    storageClassName: standard
  status:
    phase: Bound

Making storage changes

First, make the desired changes to the disk outside of the cluster. (Resize the disk in gke, or create a new disk from a snapshot or clone, etc).

How you do this, and whether or not it can be done live, without downtime, is dependant on the storage solutions you are using, and can’t be covered by this document.

Next, evaluate whether you need these changes to be reflected in the Kubernetes objects. For example: with expanding the disk storage size, the storage size settings in the PersistentVolumeClaim will only be used when a new volume resource is requested. So you would only need to increase the values in the PersistentVolumeClaim if you intend to scale up more disks (for use in additional gitaly pods).

If you do need to have the changes reflected in Kubernetes, be sure that you’ve updated your reclaim policy on the volumes as described in the Before making storage changes section.

The paths we have documented for storage changes are:

Changes to an existing Volume

First locate the volume name you are changing.

Use kubectl edit to make the desired config changes to the volume. (These changes should only be updates to reflect the real state of the attached disk)

For example:

$ kubectl --namespace helm-charts-win edit PersistentVolume pvc-6247502b-8c2d-11e8-8267-42010a9a0113
Editing Output: 

  # Please edit the object below. Lines beginning with a '#' will be ignored,
  # and an empty file will abort the edit. If an error occurs while saving this file will be
  # reopened with the relevant failures.
  #
  apiVersion: v1
  kind: PersistentVolume
  metadata:
    annotations:
      kubernetes.io/createdby: gce-pd-dynamic-provisioner
      pv.kubernetes.io/bound-by-controller: "yes"
      pv.kubernetes.io/provisioned-by: kubernetes.io/gce-pd
    creationTimestamp: 2018-07-20T14:58:43Z
    labels:
      failure-domain.beta.kubernetes.io/region: europe-west2
      failure-domain.beta.kubernetes.io/zone: europe-west2-b
    name: pvc-6247502b-8c2d-11e8-8267-42010a9a0113
    resourceVersion: "48362431"
    selfLink: /api/v1/persistentvolumes/pvc-6247502b-8c2d-11e8-8267-42010a9a0113
    uid: 650bd649-8c2d-11e8-8267-42010a9a0113
  spec:
    accessModes:
    - ReadWriteOnce
    capacity:
      # Updated the storage size
      storage: 100Gi
    claimRef:
      apiVersion: v1
      kind: PersistentVolumeClaim
      name: repo-data-review-update-app-h8qogp-gitaly-0
      namespace: helm-charts-win
      resourceVersion: "48362307"
      uid: 6247502b-8c2d-11e8-8267-42010a9a0113
    gcePersistentDisk:
      fsType: ext4
      pdName: gke-cloud-native-81a17-pvc-6247502b-8c2d-11e8-8267-42010a9a0113
    persistentVolumeReclaimPolicy: Retain
    storageClassName: standard
  status:
    phase: Bound


Now that the changes have been reflected in the volume, we need to update the claim.

Follow the instructions in the Make changes to the PersistentVolumeClaim section.

Update the volume to bind to the claim

In a separate terminal, start watching to see when the claim has its status change to bound, and then move onto the next step to make the volume available for use in the new claim.

kubectl --namespace <namespace> get --watch PersistentVolumeClaim <claim name>

Edit the volume to make it available to the new claim. Remove the .spec.claimRef section.

kubectl --namespace <namespace> edit PersistentVolume <volume name>
Editing Output: 

  # Please edit the object below. Lines beginning with a '#' will be ignored,
  # and an empty file will abort the edit. If an error occurs while saving this file will be
  # reopened with the relevant failures.
  #
  apiVersion: v1
  kind: PersistentVolume
  metadata:
    annotations:
      kubernetes.io/createdby: gce-pd-dynamic-provisioner
      pv.kubernetes.io/bound-by-controller: "yes"
      pv.kubernetes.io/provisioned-by: kubernetes.io/gce-pd
    creationTimestamp: 2018-07-20T14:58:43Z
    labels:
      failure-domain.beta.kubernetes.io/region: europe-west2
      failure-domain.beta.kubernetes.io/zone: europe-west2-b
    name: pvc-6247502b-8c2d-11e8-8267-42010a9a0113
    resourceVersion: "48362431"
    selfLink: /api/v1/persistentvolumes/pvc-6247502b-8c2d-11e8-8267-42010a9a0113
    uid: 650bd649-8c2d-11e8-8267-42010a9a0113
  spec:
    accessModes:
    - ReadWriteOnce
    capacity:
      storage: 100Gi
    gcePersistentDisk:
      fsType: ext4
      pdName: gke-cloud-native-81a17-pvc-6247502b-8c2d-11e8-8267-42010a9a0113
    persistentVolumeReclaimPolicy: Retain
    storageClassName: standard
  status:
    phase: Released


Shortly after making the change to the Volume, the terminal watching the claim status should show Bound.

Finally, apply the changes to the GitLab chart

Switching to a different Volume

If you want to switch to using a new volume, using a disk that has a copy of the appropriate data from the old volume, then first you need to create the the new Persistent Volume in Kubernetes.

In order to create a Persistent Volume for your disk, you will need to locate the driver specific documentation for your storage type.

There are a couple of things to keep in mind when following the driver documentation:

  • You need to use the driver to create a Persistent Volume, not a Pod object with a volume as shown in a lot of the documentation.
  • You do not want to create a PersistentVolumeClaim for the volume, we will be editing the existing claim instead.

The driver documentation often includes examples for using the driver in a Pod, for example:

apiVersion: v1
kind: Pod
metadata:
  name: test-pd
spec:
  containers:
  - image: k8s.gcr.io/test-webserver
    name: test-container
    volumeMounts:
    - mountPath: /test-pd
      name: test-volume
  volumes:
  - name: test-volume
    # This GCE PD must already exist.
    gcePersistentDisk:
      pdName: my-data-disk
      fsType: ext4

What you actually want, is to create a Persistent Volume, like so:

apiVersion: v1
kind: PersistentVolume
metadata:
  name: test-volume
spec:
  capacity:
    storage: 400Gi
  accessModes:
  - ReadWriteOnce
  gcePersistentDisk:
    pdName: my-data-disk
    fsType: ext4

You normally create a local yaml file with the PersistentVolume information, then issue a create command to Kubernetes to create the object using the file.

kubectl --namespace <your namespace> create -f <local-pv-file>.yaml

Once your volume is created, you can move on to Making changes to the PersistentVolumeClaim

Make changes to the PersistentVolumeClaim

Find the PersistentVolumeClaim you want to change.

kubectl --namespace <namespace> get PersistentVolumeClaims -l release=<chart release name> -ojsonpath='{range .items[*]}{.metadata.name}{"\t"}{.metadata.labels.app}{"\n"}{end}'
  • <namespace> should be replaced with the namespace where you installed the GitLab chart.
  • <chart release name> should be replaced with the name you used to install the GitLab chart.

The command will print a list of the PersistentVolumeClaim names, followed by the name of the service they are for.

Then save a copy of the claim to your local filesystem:

kubectl --namespace <namespace> get PersistentVolumeClaim <claim name> -o yaml > <claim name>.bak.yaml
Example Output: 

  apiVersion: v1
  kind: PersistentVolumeClaim
  metadata:
    annotations:
      pv.kubernetes.io/bind-completed: "yes"
      pv.kubernetes.io/bound-by-controller: "yes"
      volume.beta.kubernetes.io/storage-provisioner: kubernetes.io/gce-pd
    creationTimestamp: 2018-07-20T14:58:38Z
    labels:
      app: gitaly
      release: review-update-app-h8qogp
    name: repo-data-review-update-app-h8qogp-gitaly-0
    namespace: helm-charts-win
    resourceVersion: "48362433"
    selfLink: /api/v1/namespaces/helm-charts-win/persistentvolumeclaims/repo-data-review-update-app-h8qogp-gitaly-0
    uid: 6247502b-8c2d-11e8-8267-42010a9a0113
  spec:
    accessModes:
    - ReadWriteOnce
    resources:
      requests:
        storage: 50Gi
    storageClassName: standard
    volumeName: pvc-6247502b-8c2d-11e8-8267-42010a9a0113
  status:
    accessModes:
    - ReadWriteOnce
    capacity:
      storage: 50Gi
    phase: Bound


Create a new yaml file for a new PVC object. Have it use the same metadata.name, metadata.labels, metadata,namespace, and spec fields. (With your updates applied). And drop the other settings:

Example:

apiVersion: v1
kind: PersistentVolumeClaim
metadata:
  labels:
    app: gitaly
    release: review-update-app-h8qogp
  name: repo-data-review-update-app-h8qogp-gitaly-0
  namespace: helm-charts-win
spec:
  accessModes:
  - ReadWriteOnce
  resources:
    requests:
      # This is our updated field
      storage: 100Gi
  storageClassName: standard
  volumeName: pvc-6247502b-8c2d-11e8-8267-42010a9a0113

Now delete the old claim:

kubectl --namespace <namespace> delete PersistentVolumeClaim <claim name>

Create the new claim:

kubectl --namespace <namespace> create PersistentVolumeClaim -f <new claim yaml file>

If you are binding to the same PersistentVolume that was previous bound to the claim, then proceed to update the volume to bind to the claim

Otherwise, if you have bound the claim to a new volume, move onto apply the changes to the GitLab chart

Apply the changes to the GitLab chart

After making changes to the PersistentVolumes and PersistentVolumeClaims, you will also want to issue a helm update with the changes applied to the chart settings as well.

See the installation storage guide for the options.

Note: If you made changes to the Gitaly volume claim, you will need to delete the Gitaly StatefulSet before you will be able to issue a helm update. This is because the StatefulSet’s Volume Template is immutable, and cannot be changed.

You can delete the statefulset without deleting the Gitaly Pods: kubectl --namespace <namespace> delete --cascade=false StatefulSet <release-name>-gitaly The helm update command will recreate the StatefulSet, which will adopt and update the Gitaly pods.

Update the chart, and include the updated configuration:

Example:

helm --namespace helm-charts-win upgrade --install review-update-app-h8qogp gitlab/gitlab \
  --set gitlab.gitaly.persistence.size=100Gi \
  <your other config settings>