Project: EDB (App Definition and Development / Database)
File: troubleshooting.md

In this page, you can find some basic information on how to troubleshoot CloudNativePG in your Kubernetes cluster deployment. !!! Hint As a Kubernetes administrator, you should have the page bookmarked! 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 , 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 before performing any potential disrupting operation On top of the mandatory `kubectl` utility, for troubleshooting, we recommend the following plugins/utilities to be available in your system: for `kubectl` , a lightweight and flexible command-line JSON processor , 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 as an alternative to `grep` or directly use and install your preferred *nix distro and use the tools mentioned above. To quickly get an overview of the cluster or installation, the `kubectl` plugin is the primary tool to use: the provides an overview of a cluster the 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 for complete instructions. 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. 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: ```sh 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

The above command issues a `pg_dump` command in custom format, which is the most versatile way to take . 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): ```sh 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 `cnpg` plugin at some stage in the future. Every resource created and controlled by CloudNativePG logs to standard output, as expected by Kubernetes, and directly in [JSON format](logging.md). As a result, you should rely on the `kubectl logs` command to retrieve logs from a given resource. For more information, type: ```shell 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 CloudNativePG. By default, the CloudNativePG operator is installed in the `cnpg-system` namespace in Kubernetes as a `Deployment` (see the for details). You can get a list of the operator pods by running: ```shell kubectl get pods -n cnpg-system ``` !!! Note Under normal circumstances, you should have one pod where the operator is running, identified by a name starting with `cnpg-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 `cnpg-controller-manager`. Collect the relevant information about the operator that is running in pod `<POD>` with: ```shell kubectl describe pod -n cnpg-system <POD> ``` Then get the logs from the same pod by running: ```shell kubectl logs -n cnpg-system <POD> ``` Get logs from all pods in CloudNativePG operator Deployment (in case you have a multi operator deployment) by running: ```shell kubectl logs -n cnpg-system \ deployment/cnpg-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: ```shell kubectl logs -n cnpg-system \ deployment/cnpg-controller-manager --all-containers=true | \ jq -r . > cnpg_logs.json ``` Get CloudNativePG operator version by using `kubectl-cnpg` plugin: ```shell kubectl-cnpg status <CLUSTER> ``` Output: ```shell Cluster in healthy state Name: cluster-example Namespace: default System ID: 7044925089871458324 PostgreSQL Image:

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 ``` You can check the status of the `<CLUSTER>` cluster in the `NAMESPACE` namespace with: ```shell kubectl get cluster -n <NAMESPACE> <CLUSTER> ``` Output: ```shell 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: ```shell kubectl get cluster -o yaml -n <NAMESPACE> <CLUSTER> ``` Another important command to gather is the `status` one, as provided by the `cnpg` plugin: ```shell kubectl cnpg 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 cnpg plugin: Promote a replica.<br /> Manage certificates.<br /> Make a rollout restart cluster to apply configuration changes.<br /> Make a reconciliation loop to reload and apply configuration changes.<br /> For more information, please see documentation. Get PostgreSQL container image version: ```shell kubectl describe cluster <CLUSTER_NAME> -n <NAMESPACE> | grep "Image Name" ``` Output: ```shell Image Name: ghcr.io/cloudnative-pg/postgresql:16.2-3 ``` !!! Note Also you can use `kubectl-cnpg status -n <NAMESPACE> <CLUSTER_NAME>` to get the same information. You can retrieve the list of instances that belong to a given PostgreSQL cluster with: ```shell kubectl get pod -l cnpg.io/cluster=<CLUSTER> -L role -n <NAMESPACE> ``` Output: ```shell 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: ```shell kubectl get pod -n <NAMESPACE> -o yaml <CLUSTER>-<N> ``` You can get all the logs for a given PostgreSQL instance with: ```shell kubectl logs -n <NAMESPACE> <CLUSTER>-<N> ``` If you want to limit the search to the PostgreSQL process only, you can run: ```shell kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | \ jq 'select(.logger=="postgres") | .record.message' ``` The following example also adds the timestamp in a user-friendly format: ```shell kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | \ jq -r 'select(.logger=="postgres") | [(.ts|strflocaltime("%Y-%m-%dT%H:%M:%S %Z")), .record.message] | @csv' ``` Check logs from a specific pod that has crashed: ```shell kubectl logs -n <NAMESPACE> --previous <CLUSTER>-<N> ``` Get FATAL errors from a specific PostgreSQL pod: ```shell kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | \ jq -r '.record | select(.error_severity == "FATAL")' ``` Output: ```json { "log_time": "2021-11-08 14:07:44.520 UTC", "username": "streamingreplica", "process_id": "68", "connection_from": "10.244.0.10:60616", "session_id":

"sessionlinenum": "1", "command_tag": "startup", "sessionstarttime": "2021-11-08 14:07:44 UTC", "virtualtransactionid": "3/75", "transaction_id": "0", "error_severity": "FATAL", "sqlstatecode": "28000", "message": "role \"streaming_replica\" does not exist", "backend_type": "walsender" } ``` Filter PostgreSQL DB error messages in logs for a specific pod: ```shell kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | jq -r '.err | select(. != null)' ``` Output: ```shell dial unix /controller/run/.s.PGSQL.5432: connect: no such file or directory ``` Get messages matching `err` word from a specific pod: ```shell kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | jq -r '.msg' | grep "err" ``` Output: ```shell 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: ```shell kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | \ jq -r '. | select(.logger == "postgres") | select(.msg != "record") | .msg' ``` Output: ```shell 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: ```shell kubectl logs -n <NAMESPACE> <CLUSTER>-<N> | \ jq -r '[.level, .ts, .logger, .msg] | join(" | ")' ``` Output: ```shell info | 1636380469.5728037 | wal-archive | Backup not configured, skip WAL archiving info | 1636383566.0664876 | postgres | record ``` You can list the backups that have been created for a named cluster with: ```shell kubectl get backup -l cnpg.io/cluster=<CLUSTER> ``` !!! Important Backup labelling has been introduced in version 1.10.0 of CloudNativePG. So only those resources that have been created with that version or a higher one will contain such a label. Sometimes is useful to double-check the StorageClass used by the cluster to have some more context during investigations or troubleshooting, like this: ```shell 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. 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: ```shell kubectl get nodes -o wide ``` Additionally, you can gather the list of nodes where the pods of a given cluster are running with: ```shell kubectl get pod -l cnpg.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 . Like many native kubernetes objects , 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

Backup: ```bash $ kubectl wait --for=condition=LastBackupSucceeded cluster/<CLUSTER-NAME> -n <NAMESPACE> ``` ContinuousArchiving: ```bash $ kubectl wait --for=condition=ContinuousArchiving cluster/<CLUSTER-NAME> -n <NAMESPACE> ``` Ready (Cluster is ready or not): ```bash $ kubectl wait --for=condition=Ready cluster/<CLUSTER-NAME> -n <NAMESPACE> ``` Below is a snippet of a `cluster.status` that contains a failing condition. ```bash $ 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 ``` CloudNativePG requires basic networking and connectivity in place. You can find more information in the section. If installing CloudNativePG 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: ``` sh kubectl get networkpolicies ``` There might be several network policies set up by the Kubernetes network administrator. ``` sh $ kubectl get networkpolicies NAME POD-SELECTOR AGE allow-prometheus cnpg.io/cluster=cluster-example 47m default-deny-ingress <none> 57m ``` 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). CloudNativePG allows you to control what to include in the core dump through the `cnpg.io/coredumpFilter` annotation. !!! Info Please refer to for more details on the standard annotations that CloudNativePG provides. By default, the `cnpg.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 . 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): ```sh 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: ```sh 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. 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 in the

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: ```shell 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: ```shell kubectl get events -n <NAMESPACE> kubectl get events -n <NAMESPACE> --sort-by=.metadata.creationTimestamp ``` 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 ), 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: ```shell 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 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 . 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: ``` text Instance Status Extraction Error: HTTP communication issue ``` As pointed out in the , 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: ``` text "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. ``` sh $ kubectl get networkpolicies NAME POD-SELECTOR AGE allow-prometheus cnpg.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: ``` sh $ kubectl get networkpolicies default-deny-ingress -o yaml <snipped> spec: podSelector: {} policyTypes: Ingress ``` In the 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. 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](https://www.postgresql.org/message-id/17757-dbdfc1f1c954a6db%40postgresql.org). 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: ``` yaml 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