CRI not taken into account in config.toml

[nneram]

Description

In my cluster I add some private registries configured with an import in the config.toml. I also configured a new default CRI "nvidia" but it does not apply.
If I remove imports = ["/etc/containerd/config.d/*.toml"] from the file it works well.

kubectl describe pod -n gpu-operator-resources

 Warning  FailedCreatePodSandBox  5s (x7 over 84s)    kubelet            Failed to create pod sandbox: rpc error: code = Unknown desc = failed to get sandbox runtime: no runtime for "nvidia" is configured

Steps to reproduce the issue

1. Add an import in config.toml : imports = ["/etc/containerd/config.d/*.toml"] with at least one file (e.g.: add registries)
2. Change default CRI
3. Applied pods with the new CRI

Describe the results you received and expected

• Received:

kubectl describe pod -n gpu-operator-resources

 Warning  FailedCreatePodSandBox  5s (x7 over 84s)    kubelet            Failed to create pod sandbox: rpc error: code = Unknown desc = failed to get sandbox runtime: no runtime for "nvidia" is configured

• Expexted:

Pods running

What version of containerd are you using?

containerd containerd.io 1.4.12 7b11cfa

Any other relevant information

sudo crictl info
W1220 10:05:32.338393    6100 util_unix.go:103] Using "/var/run/containerd/containerd.sock" as endpoint is deprecated, please consider using full url format "unix:///var/run/containerd/containerd.sock".
{
  "status": {
    "conditions": [
      {
        "type": "RuntimeReady",
        "status": true,
        "reason": "",
        "message": ""
      },
      {
        "type": "NetworkReady",
        "status": true,
        "reason": "",
        "message": ""
      }
    ]
  },
  "cniconfig": {
    "PluginDirs": [
      "/opt/cni/bin"
    ],
    "PluginConfDir": "/etc/cni/net.d",
    "PluginMaxConfNum": 1,
    "Prefix": "eth",
    "Networks": [
      {
        "Config": {
          "Name": "cni-loopback",
          "CNIVersion": "0.3.1",
          "Plugins": [
            {
              "Network": {
                "type": "loopback",
                "ipam": {},
                "dns": {}
              },
              "Source": "{\"type\":\"loopback\"}"
            }
          ],
          "Source": "{\n\"cniVersion\": \"0.3.1\",\n\"name\": \"cni-loopback\",\n\"plugins\": [{\n  \"type\": \"loopback\"\n}]\n}"
        },
        "IFName": "lo"
      },
      {
        "Config": {
          "Name": "k8s-pod-network",
          "CNIVersion": "0.3.1",
          "Plugins": [
            {
              "Network": {
                "type": "calico",
                "ipam": {
                  "type": "calico-ipam"
                },
                "dns": {}
              },
              "Source": "{\"datastore_type\":\"kubernetes\",\"ipam\":{\"type\":\"calico-ipam\"},\"kubernetes\":{\"kubeconfig\":\"/etc/cni/net.d/calico-kubeconfig\"},\"log_file_path\":\"/var/log/calico/cni/cni.log\",\"log_level\":\"info\",\"mtu\":1440,\"nodename\":\"b02855srv\",\"policy\":{\"type\":\"k8s\"},\"type\":\"calico\"}"
            },
            {
              "Network": {
                "type": "portmap",
                "capabilities": {
                  "portMappings": true
                },
                "ipam": {},
                "dns": {}
              },
              "Source": "{\"capabilities\":{\"portMappings\":true},\"snat\":true,\"type\":\"portmap\"}"
            },
            {
              "Network": {
                "type": "bandwidth",
                "capabilities": {
                  "bandwidth": true
                },
                "ipam": {},
                "dns": {}
              },
              "Source": "{\"capabilities\":{\"bandwidth\":true},\"type\":\"bandwidth\"}"
            }
          ],
          "Source": "{\n  \"name\": \"k8s-pod-network\",\n  \"cniVersion\": \"0.3.1\",\n  \"plugins\": [\n    {\n      \"type\": \"calico\",\n      \"log_level\": \"info\",\n      \"log_file_path\": \"/var/log/calico/cni/cni.log\",\n      \"datastore_type\": \"kubernetes\",\n      \"nodename\": \"b02855srv\",\n      \"mtu\": 1440,\n      \"ipam\": {\n          \"type\": \"calico-ipam\"\n      },\n      \"policy\": {\n          \"type\": \"k8s\"\n      },\n      \"kubernetes\": {\n          \"kubeconfig\": \"/etc/cni/net.d/calico-kubeconfig\"\n      }\n    },\n    {\n      \"type\": \"portmap\",\n      \"snat\": true,\n      \"capabilities\": {\"portMappings\": true}\n    },\n    {\n      \"type\": \"bandwidth\",\n      \"capabilities\": {\"bandwidth\": true}\n    }\n  ]\n}"
        },
        "IFName": "eth0"
      }
    ]
  },
  "config": {
    "containerd": {
      "snapshotter": "overlayfs",
      "defaultRuntimeName": "runc",
      "defaultRuntime": {
        "runtimeType": "",
        "runtimeEngine": "",
        "PodAnnotations": null,
        "ContainerAnnotations": null,
        "runtimeRoot": "",
        "options": null,
        "privileged_without_host_devices": false,
        "baseRuntimeSpec": ""
      },
      "untrustedWorkloadRuntime": {
        "runtimeType": "",
        "runtimeEngine": "",
        "PodAnnotations": null,
        "ContainerAnnotations": null,
        "runtimeRoot": "",
        "options": null,
        "privileged_without_host_devices": false,
        "baseRuntimeSpec": ""
      },
      "runtimes": {
        "runc": {
          "runtimeType": "io.containerd.runc.v2",
          "runtimeEngine": "",
          "PodAnnotations": null,
          "ContainerAnnotations": null,
          "runtimeRoot": "",
          "options": {},
          "privileged_without_host_devices": false,
          "baseRuntimeSpec": ""
        }
      },
      "noPivot": false,
      "disableSnapshotAnnotations": true,
      "discardUnpackedLayers": false
    },
    "cni": {
      "binDir": "/opt/cni/bin",
      "confDir": "/etc/cni/net.d",
      "maxConfNum": 1,
      "confTemplate": ""
    },
    "registry": {
      "mirrors": {
        "docker.io": {
          "endpoint": [
            "https://registry-1.docker.io"
          ]
        },
        "docker-virtual.repository.com": {
          "endpoint": [
            "http://docker-virtual.repository.com"
          ]
        }
      },
      "configs": {
        "docker-virtual.repositor.com": {
          "auth": {
            "username": "user",
            "password": "some",
            "auth": "",
            "identitytoken": ""
          },
          "tls": {
            "insecure_skip_verify": true,
            "caFile": "",
            "certFile": "",
            "keyFile": ""
          }
        }
      },
      "auths": null,
      "headers": null
    },
    "imageDecryption": {
      "keyModel": ""
    },
    "disableTCPService": true,
    "streamServerAddress": "127.0.0.1",
    "streamServerPort": "0",
    "streamIdleTimeout": "4h0m0s",
    "enableSelinux": false,
    "selinuxCategoryRange": 1024,
    "sandboxImage": "k8s.gcr.io/pause:3.2",
    "statsCollectPeriod": 10,
    "systemdCgroup": false,
    "enableTLSStreaming": false,
    "x509KeyPairStreaming": {
      "tlsCertFile": "",
      "tlsKeyFile": ""
    },
    "maxContainerLogSize": 16384,
    "disableCgroup": false,
    "disableApparmor": false,
    "restrictOOMScoreAdj": false,
    "maxConcurrentDownloads": 3,
    "disableProcMount": false,
    "unsetSeccompProfile": "",
    "tolerateMissingHugetlbController": true,
    "disableHugetlbController": true,
    "ignoreImageDefinedVolumes": false,
    "containerdRootDir": "/var/lib/containerd",
    "containerdEndpoint": "/run/containerd/containerd.sock",
    "rootDir": "/var/lib/containerd/io.containerd.grpc.v1.cri",
    "stateDir": "/run/containerd/io.containerd.grpc.v1.cri"
  },
  "golang": "go1.16.10",
  "lastCNILoadStatus": "OK"
}

uname -a
Linux b02855srv 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:11 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Show configuration if it is related to CRI plugin.

cat /etc/containerd/config.toml

disabled_plugins = []
imports = ["/etc/containerd/config.d/*.toml"]
oom_score = 0
plugin_dir = ""
required_plugins = []
root = "/var/lib/containerd"
state = "/run/containerd"
version = 2

[cgroup]
  path = ""

[debug]
  address = ""
  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_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"]
    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
    ignore_image_defined_volumes = false
    max_concurrent_downloads = 3
    max_container_log_line_size = 16384
    restrict_oom_score_adj = false
    sandbox_image = "k8s.gcr.io/pause:3.2"
    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 = ""
      max_conf_num = 1

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

      [plugins."io.containerd.grpc.v1.cri".containerd.default_runtime]
        base_runtime_spec = ""
        privileged_without_host_devices = false
        runtime_engine = ""
        runtime_root = ""
        runtime_type = ""

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

        [plugins."io.containerd.grpc.v1.cri".containerd.runtimes.nvidia]
          base_runtime_spec = ""
          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/local/nvidia/toolkit/nvidia-container-runtime"
            SystemdCgroup = true

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

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

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

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

      [plugins."io.containerd.grpc.v1.cri".containerd.untrusted_workload_runtime]
        base_runtime_spec = ""
        privileged_without_host_devices = false
        runtime_engine = ""
        runtime_root = ""
        runtime_type = ""

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

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

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

        [plugins."io.containerd.grpc.v1.cri".registry.mirrors."docker.io"]
          endpoint = ["https://registry-1.docker.io"]

    [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.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"]

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

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

[timeouts]
  "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

[nneram]

This seem related to #5837.

I think that this behavior, even if it was expected in the first place, can be considered as a bug.