Known issues with NCN health checks

  • The first pass of running these tests may fail due to cloud-init not being completed on the storage nodes. In the case of failure, wait for five minutes and rerun the tests.

  • Some of the tests will fail if the Cray CLI is not configured on the management NCNs. See Cray command line interface.

  • For any failures related to SSL certificates, see the SSL Certificate Validation Issues troubleshooting guide.

  • Kubernetes Query BSS Cloud-init for ca-certs

    • This test may fail immediately after platform installation. It should pass after the TrustedCerts operator has updated BSS (Global cloud-init meta) with CA certificates.

  • Kubernetes Velero No Failed Backups

    • Because of a known issue with Velero, a backup may be attempted immediately upon the deployment of a backup schedule (for example, Vault). It may be necessary to delete backups from a Kubernetes node to clear this situation. For more information on how to clean up backups that have failed due to a known interruption, see the output of the test. For example:

      1. (ncn-mw# or pit#) Find the failed backup.

        kubectl get backups -A -o json | jq -e '.items[] | select(.status.phase == "PartiallyFailed") | .metadata.name'

      2. (ncn-mw#) Delete the backup.

        In the following command, replace <backup> with a backup returned in the previous step.

        This command will not work on the PIT node.

        velero backup delete <backup> --confirm

  • Verify spire-agent is enabled and running

    • The spire-agent service may fail to start on Kubernetes NCNs (all worker and master nodes). In this case, it may log errors (using journalctl) similar to join token does not exist or has already been used, or the last log entries may contain multiple instances of systemd[1]: spire-agent.service: Start request repeated too quickly.. Deleting the request-ncn-join-token daemonset pod running on the node may clear the issue. Even though the spire-agent systemctl service on the Kubernetes node should eventually restart cleanly, the user may have to log in to the impacted nodes and restart the service. The following recovery procedure can be run from any Kubernetes node in the cluster.

      1. (ncn-mw# or pit#) Define the following function

        function renewncnjoin() {
    for pod in $(kubectl get pods -n spire |grep request-ncn-join-token | awk '{print $1}'); do
        if kubectl describe -n spire pods $pod | grep -q "Node:.*$1"; then
            echo "Restarting $pod running on $1"
            kubectl delete -n spire pod "$pod"
        fi
    done
}

      2. (ncn-mw# or pit#) Run the function as follows (substituting the name of the impacted NCN):

        renewncnjoin ncn-xxxx

    • The spire-agent service may also fail if an NCN was powered off for too long and its tokens are expired. If this happens, delete /var/lib/spire/agent_svid.der, /var/lib/spire/bundle.der, and /var/lib/spire/data/keys.json off the NCN before deleting the request-ncn-join-token daemon set pod.

  • cfs-state-reporter service ran successfully

    • If this test is failing, it could be due to SSL certificate issues on that NCN.

      1. (ncn#) Run the following command on the node where the test is failing.

        systemctl status cfs-state-reporter | grep HTTPSConnectionPool

      2. If the previous command gives any output, this indicates possible SSL certificate problems on that NCN.

    • If this test is failing on a storage node, it could be an issue with the node’s Spire token. The following procedure may resolve the problem:

      1. (ncn-m002#) Run the following script:

        /opt/cray/platform-utils/spire/fix-spire-on-storage.sh

      2. Rerun the check to see if the problem is resolved.

  • Clock skew test failures

    It can take up to 15 minutes, and sometimes longer, for NCN clocks to synchronize after an upgrade or when a system is restored. If a clock skew test fails, wait for 15 minutes, and try again.

    (ncn-m001#) To check status, run the following command, preferably on ncn-m001:

    chronyc sources -v

    210 Number of sources = 9

  .-- Source mode  '^' = server, '=' = peer, '#' = local clock.
 / .- Source state '*' = current synced, '+' = combined , '-' = not combined,
| /   '?' = unreachable, 'x' = time may be in error, '~' = time too variable.
||                                                 .- xxxx [ yyyy ] +/- zzzz
||      Reachability register (octal) -.           |  xxxx = adjusted offset,
||      Log2(Polling interval) --.      |          |  yyyy = measured offset,
||                                \     |          |  zzzz = estimated error.
||                                 |    |           \
MS Name/IP address         Stratum Poll Reach LastRx Last sample
===============================================================================
^* ntp.hpecorp.net               2  10   377   650   -421us[ -571us] +/-   30ms
=? ncn-m002.nmn                 10   4   377   213    +82us[  +82us] +/-  367us
=- ncn-m003.nmn                  3   1   377     1  -2033us[-2033us] +/-   28ms
=- ncn-s001.nmn                  6   5   377    20    +53us[  +53us] +/-  193us
=- ncn-s002.nmn                  5   5   377    25    +29us[  +29us] +/-  275us
=- ncn-s003.nmn                  6   6   377    27    +47us[  +47us] +/-  237us
=- ncn-w001.nmn                  5   9   377  234m  +8305us[  +10ms] +/-   38ms
=- ncn-w002.nmn                  3   5   377     8  -1910us[-1910us] +/-   27ms
=- ncn-w003.nmn                  3   8   377   74m  -1122us[-1002us] +/-   31ms

  • Etcd backups missing after system power up

    After system power up, automated Etcd backups will resume within about 24 hours of the cluster being back up. When running the ncnHealthChecks.sh script within this time period, it may report a failure:

    --- FAILED --- not all Etcd clusters had expected backups.

    This is normal, and backups should resume after 24 hours.