trobleshooting k8

Installing Kubernetes on DGX using Kubeadm (Updated for TAO 5.0.0)

Created : 18/05/2023
Status: Draft

DNS within the K8 cluster not working for a node.

Setting up a new cluster

If you experience container crash loops after the initial cluster installation or after installing a CNI, the containerd configuration provided with the package might contain incompatible configuration parameters. Consider resetting the containerd configuration with

containerd config default > /etc/containerd/config.toml

as specified in this getting-started.md and then set the configuration parameters specified above accordingly.

sudo sh -c 'containerd config default > /etc/containerd/config.toml'

get logs for the unit containerd.

journalctl -xeu containerd

Forwarding IPv4 and letting iptables see bridged traffic

cat <<EOF | sudo tee /etc/modules-load.d/k8s.conf
overlay
br_netfilter
EOF

sudo modprobe overlay
sudo modprobe br_netfilter

sysctl params required by setup, params persist across reboots

cat <<EOF | sudo tee /etc/sysctl.d/k8s.conf
net.bridge.bridge-nf-call-iptables  = 1
net.bridge.bridge-nf-call-ip6tables = 1
net.ipv4.ip_forward                 = 1
EOF

Apply sysctl params without reboot

sudo sysctl --system

Verify that the br_netfilter, overlay modules are loaded by running the following commands:

lsmod | grep br_netfilter
lsmod | grep overlay

Verify that the net.bridge.bridge-nf-call-iptables, net.bridge.bridge-nf-call-ip6tables, and net.ipv4.ip_forward system variables are set to 1 in your sysctl config by running the following command:

sysctl net.bridge.bridge-nf-call-iptables net.bridge.bridge-nf-call-ip6tables net.ipv4.ip_forward

Configuring docker with nvidia container runtime

This command below will automatically modify the /etc/docker/daemon.json file to include

{
    "runtimes": {
        "nvidia": {
            "args": [],
            "path": "nvidia-container-runtime",
        }
    }
}

Command: sudo nvidia-ctk runtime configure --runtime=docker

configuring containerd

sudo nvidia-ctk runtime configure --runtime=containerd

Manual configuration

As shown in this nvidia guide we can manually do the steps above by modifying the /etc/docker/daemon.json

{
    "default-runtime": "nvidia",
    "runtimes": {
        "nvidia": {
            "args": [],
            "path": "nvidia-container-runtime",
            "runtimeArgs": []
        }
    }
}

restart the docker daemon

sudo systemctl restart docker

and update /etc/containerd/config.toml with

version = 2
[plugins]
  [plugins."io.containerd.grpc.v1.cri"]
    [plugins."io.containerd.grpc.v1.cri".containerd]
      default_runtime_name = "nvidia"

      [plugins."io.containerd.grpc.v1.cri".containerd.runtimes]
        [plugins."io.containerd.grpc.v1.cri".containerd.runtimes.nvidia]
          privileged_without_host_devices = false
          runtime_engine = ""
          runtime_root = ""
          runtime_type = "io.containerd.runc.v2"
          [plugins."io.containerd.grpc.v1.cri".containerd.runtimes.nvidia.options]
            BinaryName = "/usr/bin/nvidia-container-runtime"

Configuring the systemd cgroup driver

To use the systemd cgroup driver in /etc/containerd/config.toml with nvidia, set

[plugins."io.containerd.grpc.v1.cri".containerd.runtimes.nvidia]
  ...
  [plugins."io.containerd.grpc.v1.cri".containerd.runtimes.nvidia.options]
    SystemdCgroup = true

set SystemdCgroup = true in runc options

  [plugins."io.containerd.grpc.v1.cri".containerd.runtimes.runc.options]
            BinaryName = ""
            CriuImagePath = ""
            CriuPath = ""
            CriuWorkPath = ""
            IoGid = 0
            IoUid = 0
            NoNewKeyring = false
            NoPivotRoot = false
            Root = ""
            ShimCgroup = ""
            SystemdCgroup = true

restart containerd daemon

sudo systemctl restart containerd

disabled_plugins = []
imports = []
oom_score = 0
plugin_dir = ""
required_plugins = []
root = "/var/lib/containerd"
state = "/run/containerd"
temp = ""
version = 2

[cgroup]
  path = ""

[debug]
  address = ""
  format = ""
  gid = 0
  level = ""
  uid = 0

[grpc]
  address = "/run/containerd/containerd.sock"
  gid = 0
  max_recv_message_size = 16777216
  max_send_message_size = 16777216
  tcp_address = ""
  tcp_tls_ca = ""
  tcp_tls_cert = ""
  tcp_tls_key = ""
  uid = 0

[metrics]
  address = ""
  grpc_histogram = false

[plugins]

  [plugins."io.containerd.gc.v1.scheduler"]
    deletion_threshold = 0
    mutation_threshold = 100
    pause_threshold = 0.02
    schedule_delay = "0s"
    startup_delay = "100ms"

  [plugins."io.containerd.grpc.v1.cri"]
    device_ownership_from_security_context = false
    disable_apparmor = false
    disable_cgroup = false
    disable_hugetlb_controller = true
    disable_proc_mount = false
    disable_tcp_service = true
    enable_selinux = false
    enable_tls_streaming = false
    enable_unprivileged_icmp = false
    enable_unprivileged_ports = false
    ignore_image_defined_volumes = false
    max_concurrent_downloads = 3
    max_container_log_line_size = 16384
    netns_mounts_under_state_dir = false
    restrict_oom_score_adj = false
    sandbox_image = "registry.k8s.io/pause:3.6"
    selinux_category_range = 1024
    stats_collect_period = 10
    stream_idle_timeout = "4h0m0s"
    stream_server_address = "127.0.0.1"
    stream_server_port = "0"
    systemd_cgroup = false
    tolerate_missing_hugetlb_controller = true
    unset_seccomp_profile = ""

    [plugins."io.containerd.grpc.v1.cri".cni]
      bin_dir = "/opt/cni/bin"
      conf_dir = "/etc/cni/net.d"
      conf_template = ""
      ip_pref = ""
      max_conf_num = 1

    [plugins."io.containerd.grpc.v1.cri".containerd]
      default_runtime_name = "nvidia"
      disable_snapshot_annotations = true
      discard_unpacked_layers = false
      ignore_rdt_not_enabled_errors = false
      no_pivot = false
      snapshotter = "overlayfs"

      [plugins."io.containerd.grpc.v1.cri".containerd.default_runtime]
        base_runtime_spec = ""
        cni_conf_dir = ""
        cni_max_conf_num = 0
        container_annotations = []
        pod_annotations = []
        privileged_without_host_devices = false
        runtime_engine = ""
        runtime_path = ""
        runtime_root = ""
        runtime_type = ""

        [plugins."io.containerd.grpc.v1.cri".containerd.default_runtime.options]

      [plugins."io.containerd.grpc.v1.cri".containerd.runtimes]

	[plugins."io.containerd.grpc.v1.cri".containerd.runtimes.nvidia]
          privileged_without_host_devices = false
          runtime_engine = ""
          runtime_root = ""
          runtime_type = "io.containerd.runc.v2"

          [plugins."io.containerd.grpc.v1.cri".containerd.runtimes.nvidia.options]
            BinaryName = "/usr/bin/nvidia-container-runtime"
            # SystemdCgroup = true


        [plugins."io.containerd.grpc.v1.cri".containerd.runtimes.runc]
          base_runtime_spec = ""
          cni_conf_dir = ""
          cni_max_conf_num = 0
          container_annotations = []
          pod_annotations = []
          privileged_without_host_devices = false
          runtime_engine = ""
          runtime_path = ""
          runtime_root = ""
          runtime_type = "io.containerd.runc.v2"

          [plugins."io.containerd.grpc.v1.cri".containerd.runtimes.runc.options]
            BinaryName = ""
            CriuImagePath = ""
            CriuPath = ""
            CriuWorkPath = ""
            IoGid = 0
            IoUid = 0
            NoNewKeyring = false
            NoPivotRoot = false
            Root = ""
            ShimCgroup = ""
            SystemdCgroup = true

      [plugins."io.containerd.grpc.v1.cri".containerd.untrusted_workload_runtime]
        base_runtime_spec = ""
        cni_conf_dir = ""
        cni_max_conf_num = 0
        container_annotations = []
        pod_annotations = []
        privileged_without_host_devices = false
        runtime_engine = ""
        runtime_path = ""
        runtime_root = ""
        runtime_type = ""

        [plugins."io.containerd.grpc.v1.cri".containerd.untrusted_workload_runtime.options]

    [plugins."io.containerd.grpc.v1.cri".image_decryption]
      key_model = "node"

    [plugins."io.containerd.grpc.v1.cri".registry]
      config_path = ""

      [plugins."io.containerd.grpc.v1.cri".registry.auths]

      [plugins."io.containerd.grpc.v1.cri".registry.configs]

      [plugins."io.containerd.grpc.v1.cri".registry.headers]

      [plugins."io.containerd.grpc.v1.cri".registry.mirrors]

    [plugins."io.containerd.grpc.v1.cri".x509_key_pair_streaming]
      tls_cert_file = ""
      tls_key_file = ""

  [plugins."io.containerd.internal.v1.opt"]
    path = "/opt/containerd"

  [plugins."io.containerd.internal.v1.restart"]
    interval = "10s"

  [plugins."io.containerd.internal.v1.tracing"]
    sampling_ratio = 1.0
    service_name = "containerd"

  [plugins."io.containerd.metadata.v1.bolt"]
    content_sharing_policy = "shared"

  [plugins."io.containerd.monitor.v1.cgroups"]
    no_prometheus = false

  [plugins."io.containerd.runtime.v1.linux"]
    no_shim = false
    runtime = "runc"
    runtime_root = ""
    shim = "containerd-shim"
    shim_debug = false

  [plugins."io.containerd.runtime.v2.task"]
    platforms = ["linux/amd64"]
    sched_core = false

  [plugins."io.containerd.service.v1.diff-service"]
    default = ["walking"]

  [plugins."io.containerd.service.v1.tasks-service"]
    rdt_config_file = ""

  [plugins."io.containerd.snapshotter.v1.aufs"]
    root_path = ""

  [plugins."io.containerd.snapshotter.v1.btrfs"]
    root_path = ""

  [plugins."io.containerd.snapshotter.v1.devmapper"]
    async_remove = false
    base_image_size = ""
    discard_blocks = false
    fs_options = ""
    fs_type = ""
    pool_name = ""
    root_path = ""

  [plugins."io.containerd.snapshotter.v1.native"]
    root_path = ""

  [plugins."io.containerd.snapshotter.v1.overlayfs"]
    root_path = ""
    upperdir_label = false

  [plugins."io.containerd.snapshotter.v1.zfs"]
    root_path = ""

  [plugins."io.containerd.tracing.processor.v1.otlp"]
    endpoint = ""
    insecure = false
    protocol = ""

[proxy_plugins]

[stream_processors]

  [stream_processors."io.containerd.ocicrypt.decoder.v1.tar"]
    accepts = ["application/vnd.oci.image.layer.v1.tar+encrypted"]
    args = ["--decryption-keys-path", "/etc/containerd/ocicrypt/keys"]
    env = ["OCICRYPT_KEYPROVIDER_CONFIG=/etc/containerd/ocicrypt/ocicrypt_keyprovider.conf"]
    path = "ctd-decoder"
    returns = "application/vnd.oci.image.layer.v1.tar"

  [stream_processors."io.containerd.ocicrypt.decoder.v1.tar.gzip"]
    accepts = ["application/vnd.oci.image.layer.v1.tar+gzip+encrypted"]
    args = ["--decryption-keys-path", "/etc/containerd/ocicrypt/keys"]
    env = ["OCICRYPT_KEYPROVIDER_CONFIG=/etc/containerd/ocicrypt/ocicrypt_keyprovider.conf"]
    path = "ctd-decoder"
    returns = "application/vnd.oci.image.layer.v1.tar+gzip"

[timeouts]
  "io.containerd.timeout.bolt.open" = "0s"
  "io.containerd.timeout.shim.cleanup" = "5s"
  "io.containerd.timeout.shim.load" = "5s"
  "io.containerd.timeout.shim.shutdown" = "3s"
  "io.containerd.timeout.task.state" = "2s"

[ttrpc]
  address = ""
  gid = 0
  uid = 0

Examining coredns pods

one of the coredns pods threw the error (but even after I disconnect extra cables the DNS problem is still there)

g@gsrv:~$ kubectl logs -n kube-system coredns-64897985d-8wzgw
[INFO] plugin/ready: Still waiting on: "kubernetes"
.:53
[INFO] plugin/reload: Running configuration MD5 = db32ca3650231d74073ff4cf814959a7
CoreDNS-1.8.6
linux/amd64, go1.17.1, 13a9191

I described the suspect pod

g@gsrv:~$ kubectl describe pod  -n kube-system coredns-64897985d-8wzgw
Name:                 coredns-64897985d-8wzgw
Namespace:            kube-system
Priority:             2000000000
Priority Class Name:  system-cluster-critical
Node:                 gsrv/172.16.1.19
Start Time:           Wed, 13 Sep 2023 18:56:46 +0000
Labels:               k8s-app=kube-dns
                      pod-template-hash=64897985d
Annotations:          <none>
Status:               Running
IP:                   10.88.0.4
IPs:
  IP:           10.88.0.4
  IP:           2001:4860:4860::4
Controlled By:  ReplicaSet/coredns-64897985d
Containers:
  coredns:
    Container ID:  containerd://6dab716085b8ee44e9c32b50f9d83defc3a22afa81a73fd78b66cb6bbf3e4db9
    Image:         k8s.gcr.io/coredns/coredns:v1.8.6
    Image ID:      k8s.gcr.io/coredns/coredns@sha256:5b6ec0d6de9baaf3e92d0f66cd96a25b9edbce8716f5f15dcd1a616b3abd590e
    Ports:         53/UDP, 53/TCP, 9153/TCP
    Host Ports:    0/UDP, 0/TCP, 0/TCP
    Args:
      -conf
      /etc/coredns/Corefile
    State:          Running
      Started:      Wed, 13 Sep 2023 18:56:50 +0000
    Ready:          True
    Restart Count:  0
    Limits:
      memory:  170Mi
    Requests:
      cpu:        100m
      memory:     70Mi
    Liveness:     http-get http://:8080/health delay=60s timeout=5s period=10s #success=1 #failure=5
    Readiness:    http-get http://:8181/ready delay=0s timeout=1s period=10s #success=1 #failure=3
    Environment:  <none>
    Mounts:
      /etc/coredns from config-volume (ro)
      /var/run/secrets/kubernetes.io/serviceaccount from kube-api-access-ljl9w (ro)
Conditions:
  Type              Status
  Initialized       True 
  Ready             True 
  ContainersReady   True 
  PodScheduled      True 
Volumes:
  config-volume:
    Type:      ConfigMap (a volume populated by a ConfigMap)
    Name:      coredns
    Optional:  false
  kube-api-access-ljl9w:
    Type:                    Projected (a volume that contains injected data from multiple sources)
    TokenExpirationSeconds:  3607
    ConfigMapName:           kube-root-ca.crt
    ConfigMapOptional:       <nil>
    DownwardAPI:             true
QoS Class:                   Burstable
Node-Selectors:              kubernetes.io/os=linux
Tolerations:                 CriticalAddonsOnly op=Exists
                             node-role.kubernetes.io/control-plane:NoSchedule
                             node-role.kubernetes.io/master:NoSchedule
                             node.kubernetes.io/not-ready:NoExecute op=Exists for 300s
                             node.kubernetes.io/unreachable:NoExecute op=Exists for 300s
Events:                      <none>
g@gsrv:~$ 

check port

Kubernetes DNS used UDP

nc -zvu 10.96.0.10  53

solution

Install cluster.
Fix .toml file.
Restart services (daemon, contianerd, docker).
Restart DGX.
Delete coredns pods (new pods will be generated by the deployment).
Try DNs resolution wiht the DNS resolution tester pods.

###

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