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Troubleshoot Embedded Cluster

This topic provides information about troubleshooting Replicated Embedded Cluster installations. For more information about Embedded Cluster, including built-in extensions and architecture, see Embedded Cluster Overview.

Troubleshoot with support bundles​

This section includes information about how to collect support bundles for Embedded Cluster installations. For more information about support bundles, see About Preflight Checks and Support Bundles.

About the default Embedded Cluster support bundle spec​

Embedded Cluster includes a default support bundle spec that collects both host- and cluster-level information:

  • The host-level information is useful for troubleshooting failures related to host configuration like DNS, networking, or storage problems.
  • Cluster-level information includes details about the components provided by Replicated, such as the Admin Console and Embedded Cluster Operator that manage install and upgrade operations. If the cluster has not installed successfully and cluster-level information is not available, then it is excluded from the bundle.

In addition to the host- and cluster-level details provided by the default Embedded Cluster spec, support bundles generated for Embedded Cluster installations also include app-level details provided by any custom support bundle specs that you included in the application release.

Generate a bundle for versions 1.17.0 and later​

For Embedded Cluster 1.17.0 and later, you can run the Embedded Cluster support-bundle command to generate a support bundle.

The support-bundle command uses the default Embedded Cluster support bundle spec to collect both cluster- and host-level information. It also automatically includes any application-specific support bundle specs in the generated bundle.

To generate a support bundle:

  1. SSH onto a controller node.

    note

    You can SSH onto a worker node to generate a support bundle that contains information specific to that node. However, when run on a worker node, the support-bundle command does not capture cluster-wide information.

  2. Run the following command:

    sudo ./APP_SLUG support-bundle

    Where APP_SLUG is the unique slug for the application.

Generate a bundle for versions earlier than 1.17.0​

For Embedded Cluster versions earlier than 1.17.0, you can generate a support bundle from the shell using the kubectl support-bundle plugin.

To generate a bundle with the support-bundle plugin, you pass the default Embedded Cluster spec to collect both cluster- and host-level information. You also pass the --load-cluster-specs flag, which discovers all support bundle specs that are defined in Secrets or ConfigMaps in the cluster. This ensures that any application-specific specs are also included in the bundle. For more information, see Discover Cluster Specs in the Troubleshoot documentation.

To generate a bundle:

  1. SSH onto a controller node.

  2. Use the Embedded Cluster shell command to start a shell with access to the cluster:

    sudo ./APP_SLUG shell

    Where APP_SLUG is the unique slug for the application.

    The output looks similar to the following:

       __4___
    _  \ \ \ \   Welcome to APP_SLUG debug shell.
    <'\ /_/_/_/   This terminal is now configured to access your cluster.
    ((____!___/) Type 'exit' (or CTRL+d) to exit.
    \0\0\0\0\/  Happy hacking.
    ~~~~~~~~~~~
    root@alex-ec-2:/home/alex# export KUBECONFIG="/var/lib/embedded-cluster/k0s/pki/admin.conf"
    root@alex-ec-2:/home/alex# export PATH="$PATH:/var/lib/embedded-cluster/bin"
    root@alex-ec-2:/home/alex# source <(kubectl completion bash)
    root@alex-ec-2:/home/alex# source /etc/bash_completion

    The appropriate kubeconfig is exported, and the location of useful binaries like kubectl and the preflight and support-bundle plugins is added to PATH.

    note

    The shell command cannot be run on non-controller nodes.

  3. Generate the support bundle using the default Embedded Cluster spec and the --load-cluster-specs flag:

    kubectl support-bundle  --load-cluster-specs /var/lib/embedded-cluster/support/host-support-bundle.yaml

View logs​

You can view logs for both Embedded Cluster and the k0s systemd service to help troubleshoot Embedded Cluster deployments.

View installation logs for Embedded Cluster​

To view installation logs for Embedded Cluster:

  1. SSH onto a controller node.

  2. Navigate to /var/log/embedded-cluster and open the .log file to view logs.

View K0s logs​

You can use the journalctl command line tool to access logs for systemd services, including k0s. For more information about k0s, see the k0s documentation.

To use journalctl to view k0s logs:

  1. SSH onto a controller node or a worker node.

  2. Use journalctl to view logs for the k0s systemd service that was deployed by Embedded Cluster.

    Examples:

    journalctl -u k0scontroller
    journalctl -u k0sworker

Access the cluster​

When troubleshooting, it can be useful to list the cluster and view logs using the kubectl command line tool. For additional suggestions related to troubleshooting applications, see Troubleshooting Applications in the Kubernetes documentation.

To access the cluster and use other included binaries:

  1. SSH into a controller node.

    note

    You cannot run the shell command on worker nodes.

  2. Use the Embedded Cluster shell command to start a shell with access to the cluster:

    sudo ./APP_SLUG shell

    Where APP_SLUG is the unique slug for the application.

    The output looks similar to the following:

       __4___
    _  \ \ \ \   Welcome to APP_SLUG debug shell.
    <'\ /_/_/_/   This terminal is now configured to access your cluster.
    ((____!___/) Type 'exit' (or CTRL+d) to exit.
     \0\0\0\0\/  Happy hacking.
    ~~~~~~~~~~~
    root@alex-ec-1:/home/alex# export KUBECONFIG="/var/lib/embedded-cluster/k0s/pki/admin.conf"
    root@alex-ec-1:/home/alex# export PATH="$PATH:/var/lib/embedded-cluster/bin"
    root@alex-ec-1:/home/alex# source <(k0s completion bash)
    root@alex-ec-1:/home/alex# source <(cat /var/lib/embedded-cluster/bin/kubectl_completion_bash.sh)
    root@alex-ec-1:/home/alex# source /etc/bash_completion

    The appropriate kubeconfig is exported, and the location of useful binaries like kubectl and Replicated’s preflight and support-bundle plugins is added to PATH.

  3. Use the available binaries as needed.

    Example:

    kubectl version
    Client Version: v1.29.1
    Kustomize Version: v5.0.4-0.20230601165947-6ce0bf390ce3
    Server Version: v1.29.1+k0s

  4. Type exit or Ctrl + D to exit the shell.

Troubleshoot errors​

This section provides troubleshooting advice for common errors.

Installation failure when NVIDIA gpu operator is included as Helm extension​

Symptom​

A release that includes that includes the NVIDIA GPU Operator as a Helm extension fails to install.

Cause​

If there are any containerd services on the host, the NVIDIA GPU Operator will generate an invalid containerd config, causing the installation to fail.

This is the result of a known issue with v24.9.x of the NVIDIA GPU Operator. For more information about the known issue, see container-toolkit does not modify the containerd config correctly when there are multiple instances of the containerd binary in the nvidia-container-toolkit repository in GitHub.

For more information about including the GPU Operator as a Helm extension, see NVIDIA GPU Operator in Configure Embedded Cluster.

Solution​

To troubleshoot:

  1. Remove any existing containerd services that are running on the host (such as those deployed by Docker).

  2. Reset and reboot the node:

    sudo ./APP_SLUG reset

    Where APP_SLUG is the unique slug for the application.

    For more information, see Reset a Node in Access and Manage Embedded Clusters.

  3. Re-install with Embedded Cluster.

Calico networking issues​

Symptom​

Symptoms of Calico networking issues can include:

  • The pod is stuck in a CrashLoopBackOff state with failed health checks:

    Warning Unhealthy 6h51m (x3 over 6h52m) kubelet Liveness probe failed: Get "http://<ip:port>/readyz": dial tcp <ip:port>: connect: no route to host
    Warning Unhealthy 6h51m (x19 over 6h52m) kubelet Readiness probe failed: Get "http://<ip:port>/readyz": dial tcp <ip:port>: connect: no route to host
    ....
    Unhealthy               pod/registry-dc699cbcf-pkkbr     Readiness probe failed: Get "https://<ip:port>/": net/http: request canceled while waiting for connection (Client.Timeout exceeded while awaiting headers)
    Unhealthy               pod/registry-dc699cbcf-pkkbr     Liveness probe failed: Get "https://<ip:port>/": net/http: request canceled while waiting for connection (Client.Timeout exceeded while awaiting headers)
    ...

  • The pod log contains an I/O timeout:

    server APIs: config.k8ssandra.io/v1beta1: Get \"https://***HIDDEN***:443/apis/config.k8ssandra.io/v1beta1\": dial tcp ***HIDDEN***:443: i/o timeout"}

Cause​

Reasons can include:

  • Pod CIDR and service CIDR overlap with the host network CIDR.

  • Incorrect kernel parameters values.

  • VXLAN traffic getting dropped. By default, Calico uses VXLAN as the overlay networking protocol, with Always mode. This mode encapsulates all pod-to-pod traffic in VXLAN packets. If for some reasons, the VXLAN packets get filtered by the network, the pod will not able to communicate with other pods.

Solution​

To troubleshoot pod CIDR and service CIDR overlapping with the host network CIDR:

  1. Run the following command to verify the pod and service CIDR:

    cat /etc/k0s/k0s.yaml | grep -i cidr
        podCIDR: 10.244.0.0/17
        serviceCIDR: 10.244.128.0/17

    The default pod CIDR is 10.244.0.0/16 and service CIDR is 10.96.0.0/12.

  2. View pod network interfaces excluding Calico interfaces, and ensure there are no overlapping CIDRs.

    ip route | grep -v cali
    default via 10.152.0.1 dev ens4 proto dhcp src 10.152.0.4 metric 100
    10.152.0.1 dev ens4 proto dhcp scope link src 10.152.0.4 metric 100
    blackhole 10.244.101.192/26 proto 80
    169.254.169.254 via 10.152.0.1 dev ens4 proto dhcp src 10.152.0.4 metric 100

  3. Reset and reboot the installation:

    sudo ./APP_SLUG reset

    Where APP_SLUG is the unique slug for the application.

    For more information, see Reset a Node in Access and Manage Embedded Clusters.

  4. Reinstall the application with different CIDRs using the --cidr flag:

    sudo ./APP_SLUG install --license license.yaml --cidr 172.16.136.0/16

    For more information, see Embedded Cluster Install Options.

Disk usage on controller nodes grows over time in airgap HA installations​

Symptom​

On a multi-node airgap installation with high availability enabled, disk usage on the controller nodes increases steadily over weeks or months. The growth continues when the application is idle and no new images are pushed.

The growth is in the SeaweedFS volumes that back the built-in registry. SeaweedFS stores this data in persistent volume claims provisioned by the openebs-hostpath storage class on the controller nodes. To confirm, run the following command for each SeaweedFS volume pod (seaweedfs-volume-0, seaweedfs-volume-1, and seaweedfs-volume-2) and compare the values over time:

kubectl exec -n seaweedfs seaweedfs-volume-0 -- du -sh /data

Where /data is the persistent volume claim that holds the volume files for that pod. Do not use df for this. The openebs-hostpath storage class does not enforce a quota, so df reports the usage of the entire node file system rather than the space that SeaweedFS uses.

If you do not address the growth, the controller nodes eventually run out of disk space. This can make the cluster unhealthy and can block application upgrades.

Cause​

The filer change logs are the cause that is present on every affected cluster. Abandoned multipart uploads can be a second contributor, depending on whether image pushes have been interrupted:

  • SeaweedFS filer change logs. The SeaweedFS master runs a maintenance cycle every 17 minutes that includes fs.meta.save and fs.meta.load, which keep the metadata of the three filers in sync. Each run writes a complete metadata snapshot to the filer change log under /topics/.system/log. Because the cycle runs on a timer, the change log grows for the life of the cluster regardless of application activity. The amount written on each cycle scales with the number of files in the registry, so the growth rate increases as the registry grows.

  • Abandoned multipart uploads. Image pushes to the built-in registry are multipart uploads. When a push is interrupted, the fragments that were already uploaded remain under /buckets/registry/.uploads and are never removed.

Embedded Cluster 2.19.10 and later adds fs.log.purge and s3.clean.uploads to the SeaweedFS maintenance cycle, which prevents further growth from both causes.

These two causes do not necessarily account for all of the growth on a given cluster. Use the measurements in the following section to see how much space the cleanup actually reclaims.

note

Upgrading to Embedded Cluster 2.19.10 or later does not reclaim the space that is already in use straight away. SeaweedFS reclaims it over time, but the timing depends on how much of each volume is unused. Use the steps in this section to reclaim the space without waiting.

Solution​

To reclaim the disk space on an existing cluster:

  1. SSH into a controller node and start the Embedded Cluster shell. See Access the cluster.

  2. Measure the space that SeaweedFS uses on each node. This command is read-only:

    for pod in seaweedfs-volume-0 seaweedfs-volume-1 seaweedfs-volume-2; do
      echo -n "$pod "
      kubectl exec -n seaweedfs $pod -- du -sh /data
    done

    Record the output so that you can compare it after the cleanup.

  3. Delete the change log entries older than seven days and the multipart uploads older than 24 hours. An upload older than 24 hours is abandoned, because registry pushes complete in minutes.

    note

    Run this step when no application install or upgrade is in progress.

    kubectl exec -i -n seaweedfs seaweedfs-master-0 -- weed shell <<'EOF'
    fs.log.purge -daysAgo 7
    s3.clean.uploads -timeAgo=24h
    EOF

  4. Vacuum the volumes to return the space to the file system. The -garbageThreshold 0.01 value makes SeaweedFS rewrite every volume that holds any unused data, so this step is the most expensive one. On a large registry it is I/O intensive and can run for a long time. The lock command blocks other weed shell administrative operations until the vacuum completes, but the registry continues to serve images.

    note

    Run this step when no application install or upgrade is in progress. On a busy cluster, run it outside of business hours.

    kubectl exec -i -n seaweedfs seaweedfs-master-0 -- weed shell <<'EOF'
    lock
    volume.vacuum -garbageThreshold 0.01
    unlock
    EOF

  5. Verify that the space was reclaimed. Repeat the measurement command and compare the values to what you recorded.

Registry images and application data are not affected by these commands. The purge removes only internal change log entries, which nothing in Embedded Cluster reads, and s3.clean.uploads removes only incomplete uploads that never became part of an image.

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