Troubleshoot the Kubernetes Operator

Get Status of a Deployed Resource

To find the status of a resource deployed with the Kubernetes Operator, invoke one of the following commands:

• For Ops Manager resource deployments:

  kubectl get <resource-name> -n <metadata.namespace> -o yaml

  • The status.applicationDatabase.phase field displays the Application Database resource deployment status.

  • The status.backup.phase displays the backup daemon resource deployment status.

  • The status.opsManager.phase field displays the Ops Manager resource deployment status.

  Note

  The Cloud Manager or Ops Manager controller watches the database resources defined in the following settings:

  • spec.backup.opLogStores

  • spec.backup.s3Stores

  • spec.backup.blockStores

• For MongoDB resource deployments:

  kubectl get mdb <resource-name> -n <metadata.namespace> -o yaml

  The status.phase field displays the MongoDB resource deployment status.

The following key-value pairs describe the resource deployment statuses:

kubectl get mdb my-replica-set -n developer -o yaml

status:
    lastTransition: "2019-01-30T10:51:40Z"
    link: http://ec2-3-84-128-187.compute-1.amazonaws.com:9080/v2/5c503a8a1b90141cbdc60a77
    members: 1
    phase: Running
    version: 4.2.2-ent

status:
  lastTransition: 2019-02-01T13:00:24Z
  link: http://ec2-34-204-36-217.compute-1.amazonaws.com:9080/v2/5c51c040d6853d1f50a51678
  members: 1
  message: 'Failed to create/update replica set in Ops Manager: Status: 400 (Bad Request),
    Detail: Something went wrong validating your Automation Config. Sorry!'
  phase: Failed
  version: 4.2.2-ent

Review the Logs

Keep and review adequate logs to help debug issues and monitor cluster activity. Use the recommended logging architecture to retain Pod logs even after a Pod is deleted.

{ "logType": "<log-type>", "contents": "<log line from a log file>" }

kubectl logs -f deployment/mongodb-enterprise-operator -n <metadata.namespace>

kubectl get pods -n <metadata.namespace>

kubectl logs <podName> -n <metadata.namespace>

kubectl logs myrs-0 -n <metadata.namespace>

kubectl logs -c mongodb-enterprise-database replica-set-0 | jq -r 'select(.logType == "mongodb-audit") | .contents'

{{{ "atype":"startup","ts":{"$date":"2023-08-30T20:43:54.649+00:00"},"uuid":{"$binary":"oDcPEY69R1yiUtpMupaXOQ==","$type":"04"},"local":{"isSystemUser":true},"remote":{"isSystemUser":true},"users":[],"roles":[],"param":{"options":{"auditLog":{"destination":"file","format":"JSON","path":"/var/log/mongodb-mms-automation/mongodb-audit.log"},"config":"/data/automation-mongod.conf","net":{"bindIp":"0.0.0.0","port":27017,"tls":{"mode":"disabled"}},"processManagement":{"fork":true},"replication":{"replSetName":"replica-set"},"storage":{"dbPath":"/data","engine":"wiredTiger"},"systemLog":{"destination":"file","path":"/var/log/mongodb-mms-automation/mongodb.log"}}},"result":0}
{"atype":"startup","ts":{"$date":"2023-08-30T20:44:05.466+00:00"},"uuid":{"$binary":"OUbUWC1DQM6k/Ih4hKZq4g==","$type":"04"},"local":{"isSystemUser":true},"remote":{"isSystemUser":true},"users":[],"roles":[],"param":{"options":{"auditLog":{"destination":"file","format":"JSON","path":"/var/log/mongodb-mms-automation/mongodb-audit.log"},"config":"/data/automation-mongod.conf","net":{"bindIp":"0.0.0.0","port":27017,"tls":{"mode":"disabled"}},"processManagement":{"fork":true},"replication":{"replSetName":"replica-set"},"storage":{"dbPath":"/data","engine":"wiredTiger"},"systemLog":{"destination":"file","path":"/var/log/mongodb-mms-automation/mongodb.log"}}},"result":0}}}

spec:
   additionalMongodConfig:
      auditLog:
         destination: file
            format: JSON
            path: /var/log/mongodb-mms-automation/mongodb-audit.log

Check Messages from the Validation Webhook

The Kubernetes Operator uses a validation Webhook to prevent users from applying invalid resource definitions. The webhook rejects invalid requests.

The ClusterRole and ClusterRoleBinding for the webhook are included in the default configuration files that you apply during the installation. To create the role and binding, you must have cluster-admin privileges.

If you create an invalid resource definition, the webhook returns a message similar to the following that describes the error to the shell:

error when creating "my-ops-manager.yaml":
admission webhook "ompolicy.mongodb.com" denied the request:
shardPodSpec field is not configurable for application databases as
it is for sharded clusters and appdb replica sets

When the Kubernetes Operator reconciles each resource, it also validates that resource. The Kubernetes Operator doesn't require the validation webhook to create or update resources.

If you omit the validation webhook, or if you remove the webhook's role and binding from the default configuration, or have insufficient privileges to run the configuration, the Kubernetes Operator issues warnings, as these are not critical errors. If the Kubernetes Operator encounters a critical error, it marks the resource as Failed.

View All MongoDB resource Specifications

To view all MongoDB resource specifications in the provided namespace:

kubectl get mdb -n <metadata.namespace>

kubectl get mdb dublin -n <metadata.namespace> -o yaml

apiVersion: mongodb.com/v1
kind: MongoDB
metadata:
  annotations:
    kubectl.kubernetes.io/last-applied-configuration: |
      {"apiVersion":"mongodb.com/v1","kind":"MongoDB","metadata":{"annotations":{},"name":"dublin","namespace":"mongodb"},"spec":{"credentials":"credentials","persistent":false,"podSpec":{"memory":"1Gi"},"project":"my-om-config","type":"Standalone","version":"4.0.0-ent"}}
  clusterDomain: ""
  creationTimestamp: 2018-09-12T17:15:32Z
  generation: 1
  name: dublin
  namespace: mongodb
  resourceVersion: "337269"
  selfLink: /apis/mongodb.com/v1/namespaces/mongodb/mongodbstandalones/dublin
  uid: 7442095b-b6af-11e8-87df-0800271b001d
spec:
  credentials: my-credentials
  type: Standalone
  persistent: false
  project: my-om-config
  version: 4.2.2-ent

Restore StatefulSet that Failed to Deploy

A StatefulSet Pod may hang with a status of Pending if it encounters an error during deployment.

Pending Pods do not automatically terminate, even if you make and apply configuration changes to resolve the error.

To return the StatefulSet to a healthy state, apply the configuration changes to the MongoDB resource in the Pending state, then delete those pods.

kubectl get pods
my-replica-set-0     1/1 Running 2 2h
my-replica-set-1     1/1 Running 2 2h
my-replica-set-2     0/1 Pending 0 2h

kubectl describe pod my-replica-set-2
<describe output omitted>
Warning FailedScheduling 15s (x3691 over 3h) default-scheduler
0/3 nodes are available: 1 node(s) had taints that the pod
didn't tolerate, 2 Insufficient memory.

vi <my-replica-set>.yaml
kubectl apply -f <my-replica-set>.yaml
kubectl delete pod my-replica-set-2

Replace a ConfigMap to Reflect Changes

If you cannot modify or redeploy an already-deployed resource ConfigMap file using the kubectl apply command, run:

kubectl replace -f <my-config-map>.yaml

This deletes and re-creates the ConfigMap resource file.

This command is useful in cases where you want to make an immediate recursive change, or you need to update resource files that cannot be updated once initialized.

Remove Kubernetes Components

kubectl delete mdb <name> -n <metadata.namespace>

kubectl delete mdb --all -n <metadata.namespace>

Create a New Persistent Volume Claim after Deleting a Pod

If you accidentally delete the MongoDB replica set Pod and its Persistent Volume Claim, the Kubernetes Operator fails to reschedule the MongoDB Pod and issues the following error message:

scheduler error: pvc not found to schedule the pod

To recover from this error, you must manually create a new PVC with the PVC object's name that corresponds to this replica set Pod, such as data-<replicaset-pod-name>.

Disable Ops Manager Feature Controls

When you manage an Ops Manager project through the Kubernetes Operator, the Kubernetes Operator places the EXTERNALLY_MANAGED_LOCK feature control policy on the project. This policy disables certain features in the Ops Manager application that might compromise your Kubernetes Operator configuration. If you need to use these blocked features, you can remove the policy through the feature controls API, make changes in the Ops Manager application, and then restore the original policy through the API.

1. Retrieve the feature control policies for your Ops Manager project.

   curl --user "{USERNAME}:{APIKEY}" --digest \
        --header "Accept: application/json" \
        --header "Content-Type: application/json" \
        --include \
        --request GET "https://{OPSMANAGER-HOST}:{PORT}/api/public/v1.0/groups/{PROJECT-ID}/controlledFeature?pretty=true"

   Save the response that the API returns. After you make changes in the Ops Manager application, you must add these policies back to the project.

   Important

   Note the highlighted fields and values in the following sample response. You must send these same fields and values in later steps when you remove and add feature control policies.

   The externalManagementSystem.version field corresponds to the Kubernetes Operator version. You must send the exact same field value in your requests later in this task.

   Your response should be similar to:

   {
    "created": "2020-02-25T04:09:42Z",
    "externalManagementSystem": {
      "name": "mongodb-enterprise-operator",
      "systemId": null,
      "version": "1.4.2"
    },
    "policies": [
      {
        "disabledParams": [],
        "policy": "EXTERNALLY_MANAGED_LOCK"
      },
      {
        "disabledParams": [],
        "policy": "DISABLE_AUTHENTICATION_MECHANISMS"
      }
    ],
    "updated": "2020-02-25T04:10:12Z"
   }

2. Update the policies array with an empty list:

   Note

   The values you provide for the externalManagementSystem object, like the externalManagementSystem.version field, must match values that you received in the response in Step 1.

   curl --user "{USERNAME}:{APIKEY}" --digest \
        --header "Accept: application/json" \
        --header "Content-Type: application/json" \
        --include \
        --request PUT "https://{OPSMANAGER-HOST}:{PORT}/api/public/v1.0/groups/{PROJECT-ID}/controlledFeature?pretty=true" \
        --data
          '{
            "externalManagementSystem": {
              "name": "mongodb-enterprise-operator",
              "systemId": null,
              "version": "1.4.2"
            },
            "policies": []
          }'

   The previously blocked features are now available in the Ops Manager application.

3. Make your changes in the Ops Manager application.

4. Update the policies array with the original feature control policies:

   Note

   The values you provide for the externalManagementSystem object, like the externalManagementSystem.version field, must match values that you received in the response in Step 1.

   curl --user "{USERNAME}:{APIKEY}" --digest \
        --header "Accept: application/json" \
        --header "Content-Type: application/json" \
        --include \
        --request PUT "https://{OPSMANAGER-HOST}:{PORT}/api/public/v1.0/groups/{PROJECT-ID}/controlledFeature?pretty=true" \
        --data
          '{
            "externalManagementSystem": {
              "name": "mongodb-enterprise-operator",
              "systemId": null,
              "version": "1.4.2"
            },
            "policies": [
              {
                "disabledParams": [],
                "policy": "EXTERNALLY_MANAGED_LOCK"
              },
              {
                "disabledParams": [],
                "policy": "DISABLE_AUTHENTICATION_MECHANISMS"
              }
            ]
          }'

   The features are now blocked again, preventing you from making further changes through the Ops Manager application. However, the Kubernetes Operator retains any changes you made in the Ops Manager application while features were available.

Remove Resources when the Kubernetes Operator Fails

When you delete a MongoDB custom resource through the Kubernetes Operator, the Kubernetes Operator handles the removal of the deployment in Cloud Manager or Ops Manager. To learn more, see Remove a MongoDB resource.

However, the removal of resources might fail in Kubernetes. For example, if the Kubernetes Operator fails before you delete the MongoDB resource, you must manually remove the deployments and delete their projects in Cloud Manager or Ops Manager.

To remove Ops Manager or Cloud Manager resources manually:

1. Disable Ops Manager feature controls.

2. Remove a deployment from Ops Manager or Cloud Manager in the project by using the UI or the API.

   Remove a deployment in the Ops Manager or Cloud Manager UI. In Ops Manager, remove a deployment from Automation and remove a deployment from Monitoring.

   In Cloud Manager, remove a deployment from Automation and remove a deployment from Monitoring.

   Alternatively, remove a deployment by using the API for updating the Automation configuration in Ops Manager or Cloud Manager with an empty configuration using the Ops Manager API request, or the Cloud Manager API request.

   Run the command similar to the following Ops Manager example:

   curl --user "{USERNAME}:{APIKEY}" --digest \
        --header "Content-Type: application/json" \
        --include \
        --request PUT "https://{OPSMANAGER-HOST}/api/public/v1.0/groups/{PROJECT-ID}/automationConfig" \
        --data '{}'

   Note

   Deleting a MongoDB resource for which you enabled backup doesn't delete the resource's snapshots. You must delete snapshots in Ops Manager, or delete snapshots in Cloud Manager.

3. Delete a project from Ops Manager or Cloud Manager by using the UI or the API. Delete a project in Ops Manager, or delete a project in the Cloud Manager.

   Alternatively, delete a project by using the Ops Manager API request, or the Cloud Manager API request.

   Run the command similar to the following Ops Manager example:

   curl --user "{USERNAME}:{APIKEY}" --digest \
        --request DELETE "{OPSMANAGER-HOST}/api/public/v1.0/groups/${PROJECT-ID}"

Debug a Failing Container

A container might fail with an error that results in Kubernetes restarting that container in a loop.

You may need to interact with that container to inspect files or run commands. This requires you to prevent the container from restarting.

1. In your preferred text editor, open the MongoDB resource you need to repair.

2. To this resource, add a podSpec collection that resembles the following.

   podSpec:
     podTemplate:
       spec:
         containers:
         - name: mongodb-enterprise-database
           command: ['sh', '-c', 'echo "Hello!" && sleep 3600' ]

   The sleep command in the spec.podSpec.podTemplate.spec instructs the container to wait for the number of seconds you specify. In this example, the container will wait for 1 hour.

3. Apply this change to the resource.

   kubectl apply -f <resource>.yaml

4. Invoke the shell inside the container.

   kubectl exec -it <pod-name> bash

Verify Correctness of Domain Names in TLS Certificates

A MongoDB replica set or sharded cluster may fail to reach the READY state if the TLS certificate is invalid.

When you configure TLS for MongoDB replica sets or sharded clusters, verify that you specify a valid certificate.

If you don't specify the correct Domain Name for each TLS certificate, the Kubernetes Operator logs may contain an error message similar to the following, where foo.svc.local is the incorrectly-specified Domain Name for the cluster member's Pod:

TLS attempt failed : x509: certificate is valid for foo.svc.local,
not mongo-0-0.mongo-0.mongodb.svc.cluster.local

Each certificate should include a valid Domain Name.

For each replica set or sharded cluster member, the Common Name, also known as the Domain Name, for that member's certificate must match the FQDN of the pod this cluster member is deployed on.

The FQDN name in each certificate has the following syntax: pod-name.service-name.namespace.svc.cluster.local. This name is different for each Pod hosting a member of the replica set or a sharded cluster.

For example, for a member of a replica set deployed on a Pod with the name rs-mongos-0-0, in the Kubernetes Operator service named mongo-0 that is created in the default mongodb namespace, the FQDN is:

rs-mongos-0-0.mongo-0.mongodb.svc.cluster.local

To check whether you have correctly configured TLS certificates:

1. Run:

   kubectl logs -f <pod_name>

2. Check for TLS-related messages in the Kubernetes Operator log files.

To learn more about TLS certificate requirements, see the prerequisites on the TLS-Encrypted Connections tab in Deploy a Replica Set or in Deploy a Sharded Cluster.

Verify the MongoDB Version when Running in Local Mode

MongoDB CustomResource may fail to reach a Running state if Ops Manager is running in Local Mode and you specify either a version of MongoDB that doesn't exist, or a valid version of MongoDB for which Ops Manager deployed in local mode did not download a corresponding MongoDB archive.

If you specify a MongoDB version that doesn't exist, or a valid MongoDB version for which Ops Manager could not download a MongoDB archive, then even though the Pods can reach the READY state, the Kubernetes Operator logs contain an error message similar to the following:

Failed to create/update (Ops Manager reconciliation phase):
Status: 400 (Bad Request), Detail:
Invalid config: MongoDB <version> is not available.

This may mean that the MongoDB Agent could not successfully download a corresponding MongoDB binary to the /var/lib/mongodb-mms-automation directory. In cases when the MongoDB Agent can download the MongoDB binary for the specified MongoDB version successfully, this directory contains a MongoDB binary folder, such as mongodb-linux-x86_64-4.4.0.

To check whether a MongoDB binary folder is present:

1. Specify the Pod's name to this command:

   kubectl exec --stdin --tty $<pod_name> /bin/sh

2. Check whether a MongoDB binary folder is present in the /var/lib/mongodb-mms-automation directory.

3. If you cannot locate a MongoDB binary folder, copy the MongoDB archive into the Ops Manager Persistent Volume for each deployed Ops Manager replica set.

Upgrade Fails Using kubectl or oc

You might receive the following error when you upgrade the Kubernetes Operator:

Forbidden: updates to statefulset spec for fields other than
'replicas', 'template', and 'updateStrategy' are forbidden

To resolve this error:

1. Remove the old Kubernetes Operator deployment.

   kubectl delete deployment/mongodb-enterprise-operator -n <metadata.namespace>

   Note

   Removing the Kubernetes Operator deployment doesn’t affect the lifecycle of your MongoDB resources.

2. Repeat the kubectl apply command to upgrade to the new version of the Kubernetes Operator.

Upgrade Fails Using Helm Charts

You might receive the following error when you upgrade the Kubernetes Operator:

Error: UPGRADE FAILED: cannot patch "mongodb-enterprise-operator"
with kind Deployment: Deployment.apps "mongodb-enterprise-operator"
is invalid: ... field is immutable

To resolve this error:

1. Remove the old Kubernetes Operator deployment.

   kubectl delete deployment/mongodb-enterprise-operator -n <metadata.namespace>

   Note

   Removing the Kubernetes Operator deployment doesn’t affect the lifecycle of your MongoDB resources.

2. Repeat the helm command to upgrade to the new version of the Kubernetes Operator.

Two Operator Instances After an Upgrade

After you upgrade from Kubernetes Operator version 1.10 or earlier to a version 1.11 or later, your Kubernetes cluster might have two instances of the Kubernetes Operator deployed.

Use the get pods command to view your Kubernetes Operator pods:

kubectl get pods

If the response contains both an enterprise-operator and a mongodb-enterprise-operator pod, your cluster has two Kubernetes Operator instances:

NAME                                           READY   STATUS    RESTARTS   AGE
enterprise-operator-767884c9b4-ltkln           1/1     Running   0          122m
mongodb-enterprise-operator-6d69686679-9fzs7   1/1     Running   0          68m

You can safely remove the enterprise-operator deployment. Run the following command to remove it:

kubectl delete deployment/enterprise-operator

Recover Resource Due to Broken Automation Configuration

If a custom resource remains in a Pending or Failed state for a longer period of time, Kubernetes Operator automatically recovers your MongoDB resources by pushing the automation configuration to Ops Manager. This prevents a deadlock when the MongoDB Agent can't push an updated automation configuration change because the StatefulSet is stuck in a Pending state due to a previous push of an invalid automation configuration.

To configure automatic recovery, define the following environmental variables in your mongodb-enterprise.yaml file:

• MDB_AUTOMATIC_RECOVERY_ENABLE to enable or disable automatic recovery for MongoDB resources per Pod.

• MDB_AUTOMATIC_RECOVERY_BACKOFF_TIME_S to set the number of seconds that a custom resource can remain in a Pending or Failed state before the Kubernetes Operator automatically recovers your MongoDB resources.

1
spec:
2
  template:
3
     spec:
4
        serviceAccountName: mongodb-enterprise-operator
5
        containers:
6
          - name: mongodb-enterprise-operator
7
            image: <operatorVersionUrl>
8
            imagePullPolicy: <policyChoice>
9
            env:
10
             - name: MDB_AUTOMATIC_RECOVERY_ENABLE
11
               value: true
12
             - name: MDB_AUTOMATIC_RECOVERY_BACKOFF_TIME_S
13
               value: 1200

To learn how to define environment variables, see Define Environment Variables for a Container.