Troubleshooting v1

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In this page, you can find some basic information on how to troubleshoot EDB Postgres for Kubernetes in your Kubernetes cluster deployment.

Hint

As a Kubernetes administrator, you should have the kubectl Cheat Sheet page bookmarked!

Before you start

Kubernetes environment

What can make a difference in a troubleshooting activity is to provide clear information about the underlying Kubernetes system.

Make sure you know:

the Kubernetes distribution and version you are using
the specifications of the nodes where PostgreSQL is running
as much as you can about the actual storage, including storage class and benchmarks you have done before going into production.
which relevant Kubernetes applications you are using in your cluster (i.e. Prometheus, Grafana, Istio, Certmanager, ...)
the situation of continuous backup, in particular if it's in place and working correctly: in case it is not, make sure you take an emergency backup before performing any potential disrupting operation

Useful utilities

On top of the mandatory kubectl utility, for troubleshooting, we recommend the following plugins/utilities to be available in your system:

cnp plugin for kubectl
jq, a lightweight and flexible command-line JSON processor
grep, searches one or more input files for lines containing a match to a specified pattern. It is already available in most *nix distros. If you are on Windows OS, you can use findstr as an alternative to grep or directly use wsl and install your preferred *nix distro and use the tools mentioned above.

First steps

To quickly get an overview of the cluster or installation, the kubectl plugin is the primary tool to use:

the status subcommand provides an overview of a cluster
the report subcommand provides the manifests for clusters and the operator deployment. It can also include logs using the --logs option. The report generated via the plugin will include the full cluster manifest.

The plugin can be installed on air-gapped systems via packages. Please refer to the plugin document for complete instructions.

Are there backups?

After getting the cluster manifest with the plugin, you should verify if backups are set up and working.

In a cluster with backups set up, you will find, in the cluster Status, the fields lastSuccessfulBackup and firstRecoverabilityPoint. You should make sure there is a recent lastSuccessfulBackup.

A cluster lacking the .spec.backup stanza won't have backups. An insistent message will appear in the PostgreSQL logs:

Backup not configured, skip WAL archiving.

Before proceeding with troubleshooting operations, it may be advisable to perform an emergency backup depending on your findings regarding backups. Refer to the following section for instructions.

It is extremely risky to operate a production database without keeping regular backups.

Emergency backup

In some emergency situations, you might need to take an emergency logical backup of the main app database.

Important

The instructions you find below must be executed only in emergency situations and the temporary backup files kept under the data protection policies that are effective in your organization. The dump file is indeed stored in the client machine that runs the kubectl command, so make sure that all protections are in place and you have enough space to store the backup file.

The following example shows how to take a logical backup of the app database in the cluster-example Postgres cluster, from the cluster-example-1 pod:

kubectl exec cluster-example-1 -c postgres \
  -- pg_dump -Fc -d app > app.dump

Note

You can easily adapt the above command to backup your cluster, by providing the names of the objects you have used in your environment.

The above command issues a pg_dump command in custom format, which is the most versatile way to take logical backups in PostgreSQL.

The next step is to restore the database. We assume that you are operating on a new PostgreSQL cluster that's been just initialized (so the app database is empty).

The following example shows how to restore the above logical backup in the app database of the new-cluster-example Postgres cluster, by connecting to the primary (new-cluster-example-1 pod):

kubectl exec -i new-cluster-example-1 -c postgres \
  -- pg_restore --no-owner --role=app -d app --verbose < app.dump

Important

The example in this section assumes that you have no other global objects (databases and roles) to dump and restore, as per our recommendation. In case you have multiple roles, make sure you have taken a backup using pg_dumpall -g and you manually restore them in the new cluster. In case you have multiple databases, you need to repeat the above operation one database at a time, making sure you assign the right ownership. If you are not familiar with PostgreSQL, we advise that you do these critical operations under the guidance of a professional support company.

The above steps might be integrated into the cnp plugin at some stage in the future.

Logs

Every resource created and controlled by EDB Postgres for Kubernetes logs to standard output, as expected by Kubernetes, and directly in JSON format. As a result, you should rely on the kubectl logs command to retrieve logs from a given resource.

For more information, type:

kubectl logs --help

Hint

JSON logs are great for machine reading, but hard to read for human beings. Our recommendation is to use the jq command to improve usability. For example, you can pipe the kubectl logs command with | jq -C.

Note

In the sections below, we will show some examples on how to retrieve logs about different resources when it comes to troubleshooting EDB Postgres for Kubernetes.

Operator information

By default, the EDB Postgres for Kubernetes operator is installed in the postgresql-operator-system namespace in Kubernetes as a Deployment (see the "Details about the deployment" section for details).

You can get a list of the operator pods by running:

kubectl get pods -n postgresql-operator-system

Note

Under normal circumstances, you should have one pod where the operator is running, identified by a name starting with postgresql-operator-controller-manager-. In case you have set up your operator for high availability, you should have more entries. Those pods are managed by a deployment named postgresql-operator-controller-manager.

Collect the relevant information about the operator that is running in pod <POD> with:

kubectl describe pod -n postgresql-operator-system <POD>

Then get the logs from the same pod by running:

kubectl logs -n postgresql-operator-system <POD>

Gather more information about the operator

Get logs from all pods in EDB Postgres for Kubernetes operator Deployment (in case you have a multi operator deployment) by running:

kubectl logs -n postgresql-operator-system \
  deployment/postgresql-operator-controller-manager --all-containers=true

Tip

You can add -f flag to above command to follow logs in real time.

Save logs to a JSON file by running:

kubectl logs -n postgresql-operator-system \
  deployment/postgresql-operator-controller-manager --all-containers=true | \
  jq -r . > cnp_logs.json

Get EDB Postgres for Kubernetes operator version by using kubectl-cnp plugin:

kubectl-cnp status <CLUSTER>

Output:

Cluster in healthy state
Name:               cluster-example
Namespace:          default
System ID:          7044925089871458324
PostgreSQL Image:   quay.io/enterprisedb/postgresql:16.1-3
Primary instance:   cluster-example-1
Instances:          3
Ready instances:    3
Current Write LSN:  0/5000000 (Timeline: 1 - WAL File: 000000010000000000000004)

Continuous Backup status
Not configured

Streaming Replication status
Name               Sent LSN   Write LSN  Flush LSN  Replay LSN  Write Lag       Flush Lag       Replay Lag      State      Sync State  Sync Priority
----               --------   ---------  ---------  ----------  ---------       ---------       ----------      -----      ----------  -------------
cluster-example-2  0/5000000  0/5000000  0/5000000  0/5000000   00:00:00        00:00:00        00:00:00        streaming  async       0
cluster-example-3  0/5000000  0/5000000  0/5000000  0/5000000   00:00:00.10033  00:00:00.10033  00:00:00.10033  streaming  async       0

Instances status
Name               Database Size  Current LSN  Replication role  Status  QoS         Manager Version
----               -------------  -----------  ----------------  ------  ---         ---------------
cluster-example-1  33 MB          0/5000000    Primary           OK      BestEffort  1.12.0
cluster-example-2  33 MB          0/5000000    Standby (async)   OK      BestEffort  1.12.0
cluster-example-3  33 MB          0/5000060    Standby (async)   OK      BestEffort  1.12.0

Cluster information

You can check the status of the <CLUSTER> cluster in the NAMESPACE namespace with:

kubectl get cluster -n <NAMESPACE> <CLUSTER>

Output:

NAME        AGE        INSTANCES   READY   STATUS                     PRIMARY
<CLUSTER>   10d4h3m    3           3       Cluster in healthy state   <CLUSTER>-1

The above example reports a healthy PostgreSQL cluster of 3 instances, all in ready state, and with <CLUSTER>-1 being the primary.

In case of unhealthy conditions, you can discover more by getting the manifest of the Cluster resource:

kubectl get cluster -o yaml -n <NAMESPACE> <CLUSTER>

Another important command to gather is the status one, as provided by the cnp plugin:

kubectl cnp status -n <NAMESPACE> <CLUSTER>

Tip

You can print more information by adding the --verbose option.

Note

Besides knowing cluster status, you can also do the following things with the cnp plugin: Promote a replica.
Manage certificates.
Make a rollout restart cluster to apply configuration changes.
Make a reconciliation loop to reload and apply configuration changes.
For more information, please see cnp plugin documentation.

Get EDB PostgreSQL Advanced Server (EPAS) / PostgreSQL container image version:

kubectl describe cluster <CLUSTER_NAME> -n <NAMESPACE> | grep "Image Name"

Output:

  Image Name:    quay.io/enterprisedb/postgresql:16.1-3

Note

Also you can use kubectl-cnp status -n <NAMESPACE> <CLUSTER_NAME> to get the same information.

Pod information

You can retrieve the list of instances that belong to a given PostgreSQL cluster with:

# using labels available from CNP 1.12.0
kubectl get pod -l k8s.enterprisedb.io/cluster=<CLUSTER> -L role -n <NAMESPACE>
# using legacy labels
kubectl get pod -l postgresql=<CLUSTER> -L role -n <NAMESPACE>

Output:

NAME          READY   STATUS    RESTARTS   AGE       ROLE
<CLUSTER>-1   1/1     Running   0          10d4h5m   primary
<CLUSTER>-2   1/1     Running   0          10d4h4m   replica
<CLUSTER>-3   1/1     Running   0          10d4h4m   replica

You can check if/how a pod is failing by running:

kubectl get pod -n <NAMESPACE> -o yaml <CLUSTER>-<N>

You can get all the logs for a given PostgreSQL instance with:

kubectl logs -n <NAMESPACE> <CLUSTER>-<N>

If you want to limit the search to the PostgreSQL process only, you can run:

kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | \
  jq 'select(.logger=="postgres") | .record.message'

The following example also adds the timestamp in a user-friendly format:

kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | \
  jq -r 'select(.logger=="postgres") | [(.ts|strflocaltime("%Y-%m-%dT%H:%M:%S %Z")), .record.message] | @csv'

Gather and filter extra information about PostgreSQL pods

Check logs from a specific pod that has crashed:

kubectl logs -n <NAMESPACE> --previous <CLUSTER>-<N>

Get FATAL errors from a specific PostgreSQL pod:

kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | \
  jq -r '.record | select(.error_severity == "FATAL")'

Output:

{
  "log_time": "2021-11-08 14:07:44.520 UTC",
  "user_name": "streaming_replica",
  "process_id": "68",
  "connection_from": "10.244.0.10:60616",
  "session_id": "61892f30.44",
  "session_line_num": "1",
  "command_tag": "startup",
  "session_start_time": "2021-11-08 14:07:44 UTC",
  "virtual_transaction_id": "3/75",
  "transaction_id": "0",
  "error_severity": "FATAL",
  "sql_state_code": "28000",
  "message": "role \"streaming_replica\" does not exist",
  "backend_type": "walsender"
}

Filter PostgreSQL DB error messages in logs for a specific pod:

kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | jq -r '.err | select(. != null)'

Output:

dial unix /controller/run/.s.PGSQL.5432: connect: no such file or directory

Get messages matching err word from a specific pod:

kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | jq -r '.msg' | grep "err"

Output:

2021-11-08 14:07:39.610 UTC [15] LOG:  ending log output to stderr

Get all logs from PostgreSQL process from a specific pod:

kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | \
  jq -r '. | select(.logger == "postgres") | select(.msg != "record") | .msg'

Output:

2021-11-08 14:07:52.591 UTC [16] LOG:  redirecting log output to logging collector process
2021-11-08 14:07:52.591 UTC [16] HINT:  Future log output will appear in directory "/controller/log".
2021-11-08 14:07:52.591 UTC [16] LOG:  ending log output to stderr
2021-11-08 14:07:52.591 UTC [16] HINT:  Future log output will go to log destination "csvlog".

Get pod logs filtered by fields with values and join them separated by | running:

kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | \
  jq -r '[.level, .ts, .logger, .msg] | join(" | ")'

Output:

info | 1636380469.5728037 | wal-archive | Backup not configured, skip WAL archiving
info | 1636383566.0664876 | postgres | record

Backup information

You can list the backups that have been created for a named cluster with:

kubectl get backup -l k8s.enterprisedb.io/cluster=<CLUSTER>

Important

Backup labelling has been introduced in version 1.10.0 of EDB Postgres for Kubernetes. So only those resources that have been created with that version or a higher one will contain such a label.

Storage information

Sometimes is useful to double-check the StorageClass used by the cluster to have some more context during investigations or troubleshooting, like this:

STORAGECLASS=$(kubectl get pvc <POD> -o jsonpath='{.spec.storageClassName}')
kubectl get storageclasses $STORAGECLASS -o yaml

We are taking the StorageClass from one of the cluster pod here since often clusters are created using the default StorageClass.

Node information

Kubernetes nodes is where ultimately PostgreSQL pods will be running. It's strategically important to know as much as we can about them.

You can get the list of nodes in your Kubernetes cluster with:

# look at the worker nodes and their status
kubectl get nodes -o wide

Additionally, you can gather the list of nodes where the pods of a given cluster are running with:

kubectl get pod -l k8s.enterprisedb.io/cluster=<CLUSTER> \
  -L role -n <NAMESPACE> -o wide

The latter is important to understand where your pods are distributed - very useful if you are using affinity/anti-affinity rules and/or tolerations.

Conditions

Like many native kubernetes objects like here, Cluster exposes status.conditions as well. This allows one to 'wait' for a particular event to occur instead of relying on the overall cluster health state. Available conditions as of now are:

LastBackupSucceeded
ContinuousArchiving
Ready

LastBackupSucceeded is reporting the status of the latest backup. If set to True the last backup has been taken correctly, it is set to False otherwise.

ContinuousArchiving is reporting the status of the WAL archiving. If set to True the last WAL archival process has been terminated correctly, it is set to False otherwise.

Ready is True when the cluster has the number of instances specified by the user and the primary instance is ready. This condition can be used in scripts to wait for the cluster to be created.

How to wait for a particular condition

Backup:

$ kubectl wait --for=condition=LastBackupSucceeded cluster/<CLUSTER-NAME> -n <NAMESPACE>

ContinuousArchiving:

$ kubectl wait --for=condition=ContinuousArchiving cluster/<CLUSTER-NAME> -n <NAMESPACE>

Ready (Cluster is ready or not):

$ kubectl wait --for=condition=Ready cluster/<CLUSTER-NAME> -n <NAMESPACE>

Below is a snippet of a cluster.status that contains a failing condition.

$ kubectl get cluster/<cluster-name> -o yaml
.
.
.
  status:
    conditions:
    - message: 'unexpected failure invoking barman-cloud-wal-archive: exit status
        2'
      reason: ContinuousArchivingFailing
      status: "False"
      type: ContinuousArchiving

    - message: exit status 2
      reason: LastBackupFailed
      status: "False"
      type: LastBackupSucceeded

    - message: Cluster Is Not Ready
      reason: ClusterIsNotReady
      status: "False"
      type: Ready

Networking

EDB Postgres for Kubernetes requires basic networking and connectivity in place. You can find more information in the networking section.

If installing EDB Postgres for Kubernetes in an existing environment, there might be network policies in place, or other network configuration made specifically for the cluster, which could have an impact on the required connectivity between the operator and the cluster pods and/or the between the pods.

You can look for existing network policies with the following command:

kubectl get networkpolicies

There might be several network policies set up by the Kubernetes network administrator.

$ kubectl get networkpolicies                       
NAME                   POD-SELECTOR                      AGE
allow-prometheus       k8s.enterprisedb.io/cluster=cluster-example   47m
default-deny-ingress   <none>                            57m

PostgreSQL core dumps

Although rare, PostgreSQL can sometimes crash and generate a core dump in the PGDATA folder. When that happens, normally it is a bug in PostgreSQL (and most likely it has already been solved - this is why it is important to always run the latest minor version of PostgreSQL).

EDB Postgres for Kubernetes allows you to control what to include in the core dump through the k8s.enterprisedb.io/coredumpFilter annotation.

Info

Please refer to "Labels and annotations" for more details on the standard annotations that EDB Postgres for Kubernetes provides.

By default, the k8s.enterprisedb.io/coredumpFilter is set to 0x31 in order to exclude shared memory segments from the dump, as this is the safest approach in most cases.

Info

Please refer to "Core dump filtering settings" section of "The /proc Filesystem" page of the Linux Kernel documentation. for more details on how to set the bitmask that controls the core dump filter.

Important

Beware that this setting only takes effect during Pod startup and that changing the annotation doesn't trigger an automated rollout of the instances.

Although you might not personally be involved in inspecting core dumps, you might be asked to provide them so that a Postgres expert can look into them. First, verify that you have a core dump in the PGDATA directory with the following command (please run it against the correct pod where the Postgres instance is running):

kubectl exec -ti POD -c postgres \
  -- find /var/lib/postgresql/data/pgdata -name 'core.*'

Under normal circumstances, this should return an empty set. Suppose, for example, that we have a core dump file:

/var/lib/postgresql/data/pgdata/core.14177

Once you have verified the space on disk is sufficient, you can collect the core dump on your machine through kubectl cp as follows:

kubectl cp POD:/var/lib/postgresql/data/pgdata/core.14177 core.14177

You now have the file. Make sure you free the space on the server by removing the core dumps.

Some common issues

Storage is full

If one or more pods in the cluster are in CrashloopBackoff and logs suggest this could be due to a full disk, you probably have to increase the size of the instance's PersistentVolumeClaim. Please look at the "Volume expansion" section in the documentation.

Pods are stuck in `Pending` state

In case a Cluster's instance is stuck in the Pending phase, you should check the pod's Events section to get an idea of the reasons behind this:

kubectl describe pod -n <NAMESPACE> <POD>

Some of the possible causes for this are:

No nodes are matching the nodeSelector
Tolerations are not correctly configured to match the nodes' taints
No nodes are available at all: this could also be related to cluster-autoscaler hitting some limits, or having some temporary issues

In this case, it could also be useful to check events in the namespace:

kubectl get events -n <NAMESPACE>
# list events in chronological order
kubectl get events -n <NAMESPACE> --sort-by=.metadata.creationTimestamp

Replicas out of sync when no backup is configured

Sometimes replicas might be switched off for a bit of time due to maintenance reasons (think of when a Kubernetes nodes is drained). In case your cluster does not have backup configured, when replicas come back up, they might require a WAL file that is not present anymore on the primary (having been already recycled according to the WAL management policies as mentioned in "The postgresql section"), and fall out of synchronization.

Similarly, when pg_rewind might require a WAL file that is not present anymore in the former primary, reporting pg_rewind: error: could not open file.

In these cases, pods cannot become ready anymore, and you are required to delete the PVC and let the operator rebuild the replica.

If you rely on dynamically provisioned Persistent Volumes, and you are confident in deleting the PV itself, you can do so with:

PODNAME=<POD>
VOLNAME=$(kubectl get pv -o json | \
  jq -r '.items[]|select(.spec.claimRef.name=='\"$PODNAME\"')|.metadata.name')

kubectl delete pod/$PODNAME pvc/$PODNAME pvc/$PODNAME-wal pv/$VOLNAME

Cluster stuck in `Creating new replica`

Cluster is stuck in "Creating a new replica", while pod logs don't show relevant problems. This has been found to be related to the next issue on connectivity. From releases 1.20.1, 1.19.3, and 1.18.5, networking issues will be more clearly reflected in the status column as follows:

Instance Status Extraction Error: HTTP communication issue

Networking is impaired by installed Network Policies

As pointed out in the networking section, local network policies could prevent some of the required connectivity.

A tell-tale sign that connectivity is impaired is the presence in the operator logs of messages like:

"Cannot extract Pod status", […snipped…] "Get \"http://<pod IP>:8000/pg/status\": dial tcp <pod IP>:8000: i/o timeout"

You should list the network policies, and look for any policies restricting connectivity.

$ kubectl get networkpolicies                       
NAME                   POD-SELECTOR                      AGE
allow-prometheus       k8s.enterprisedb.io/cluster=cluster-example   47m
default-deny-ingress   <none>                            57m

For example, in the listing above, default-deny-ingress seems a likely culprit. You can drill into it:

$ kubectl get networkpolicies default-deny-ingress -o yaml
<…snipped…>
spec:
  podSelector: {}
  policyTypes:
  - Ingress

In the networking page you can find a network policy file that you can customize to create a NetworkPolicy explicitly allowing the operator to connect cross-namespace to cluster pods.

Error while bootstrapping the data directory

If your Cluster's initialization job crashes with a "Bus error (core dumped) child process exited with exit code 135", you likely need to fix the Cluster hugepages settings.

The reason is the incomplete support of hugepages in the cgroup v1 that should be fixed in v2. For more information, check the PostgreSQL BUG #17757: Not honoring huge_pages setting during initdb causes DB crash in Kubernetes.

To check whether hugepages are enabled, run grep HugePages /proc/meminfo on the Kubernetes node and check if hugepages are present, their size, and how many are free.

If the hugepages are present, you need to configure how much hugepages memory every PostgreSQL pod should have available.

For example:

  postgresql:
    parameters:
      shared_buffers: "128MB"

  resources:
    requests:
      memory: "512Mi"
    limits:
      hugepages-2Mi: "512Mi"

Please remember that you must have enough hugepages memory available to schedule every Pod in the Cluster (in the example above, at least 512MiB per Pod must be free).

Troubleshooting v1

Hint

Before you start

Kubernetes environment

Useful utilities

First steps

Are there backups?

Emergency backup

Important

Note

Important

Logs

Hint

Note

Operator information

Note

Gather more information about the operator

Tip

Cluster information

Tip

Note

Note

Pod information

Gather and filter extra information about PostgreSQL pods

Backup information

Important

Storage information

Node information

Conditions

How to wait for a particular condition

Networking

PostgreSQL core dumps

Info

Info

Important

Some common issues

Storage is full

Pods are stuck in Pending state

Replicas out of sync when no backup is configured

Cluster stuck in Creating new replica

Networking is impaired by installed Network Policies

Error while bootstrapping the data directory

Pods are stuck in `Pending` state

Cluster stuck in `Creating new replica`