I found this issue is related to a bug in docker-entrypoint.sh and occurs when numactl is detected on the node.

Try this simplified code (which moves numactl out of the way):

apiVersion: apps/v1
kind: Deployment
metadata:
  name: mongo-deployment
  labels:
    app: mongo
spec:
  replicas: 1
  selector:
    matchLabels:
      app: mongo
  template:
    metadata:
      labels:
        app: mongo
    spec:
      containers:
      - name: mongo
        image: mongo:4.0.0
        command:
        - /bin/bash
        - -c
        # mv is not needed for later versions e.g. 3.4.19 and 4.1.7
        - mv /usr/bin/numactl /usr/bin/numactl1 && source docker-entrypoint.sh mongod
        env:
        - name: MONGO_INITDB_ROOT_USERNAME
          value: "xxxxx"
        - name: MONGO_INITDB_ROOT_PASSWORD
          value: "xxxxx"
        ports:
        - containerPort: 27017

I raised an issue at: https://github.com/docker-library/mongo/issues/330

Hopefully it will be fixed at some point so no need for the hack :o)

The reason the environment variables don't work is that the MONGO_INITDB environment variables are used by the docker-entrypoint.sh script within the image ( https://github.com/docker-library/mongo/tree/master/4.0 ) however when you define a 'command:' in your kubernetes file you override that entrypoint (see notes https://kubernetes.io/docs/tasks/inject-data-application/define-command-argument-container/ )

See below YML which is adapted from a few of the examples I found online. Note the learning points for me

1. cvallance/mongo-k8s-sidecar looks for ANY mongo instance matching the POD labels REGARDLESS of namespace so it'll try to hook up with any old instance in the cluster. This caused me a few hours of headscratching as I'd removed the environment= labels from the example as we use namespaces to segregate our environments..silly and obvious in retrospect...extremely confusing in the beginning (mongo logs were throwing all sorts of authentication errors and service down type errors because of the cross talk)

2. I was new to ClusterRoleBindings and it took me a while to realise they are Cluster level which I know seems obvious (despite needing to supply a namespace to get kubectl to accept it) but was causing mine to get overwritten between each namespace so make sure you create unique names per environment to avoid a deployment in one namespace messing up another as the ClusterRoleBinding gets overwritten if they're not unqiue within the cluster

3. MONGODB_DATABASE needs to be set to 'admin' for authentication to work.

4. I was following this example to configure authentication which depended on a sleep5 in the hope the daemon was up and running before attempting to create the adminUser. I found this wasn't long enough so upped it initially as failure to create the adminUser obviously led to connection refused issues. I later changed the sleep to test the daemon with a while loop and a ping of mongo which is more foolproof.

5. If you run mongod in a container (e.g. lxc, cgroups, Docker, etc.) that does not have access to all of the RAM available in a system, you must set --wiredTigerCacheSizeGB to a value less than the amount of RAM available in the container. The exact amount depends on the other processes running in the container.

   6. You need at least 3 nodes in a Mongo cluster !

The YML below should spin up and configure a mongo replicaset in kubernetes with persistent storage and authentication enabled. If you connect into the pod...

kubectl exec -ti mongo-db-0 --namespace somenamespace /bin/bash

mongo shell is installed in the image so you should be able to connect to the replicaset with...

mongo mongodb://mongoadmin:adminpassword@mongo-db/admin?replicaSet=rs0

And see that you get either rs0:PRIMARY> or rs0:SECONDARY, indicating the two pods are in a mongo replicateset. use rs.conf() to verify that from the PRIMARY.

#Create a Secret to hold the MONGO_INITDB_ROOT_USERNAME/PASSWORD
#so we can enable authentication
apiVersion: v1
data:
     #echo -n "mongoadmin" | base64
    init.userid: bW9uZ29hZG1pbg==
    #echo -n "adminpassword" | base64
    init.password: YWRtaW5wYXNzd29yZA==
kind: Secret
metadata:
  name: mongo-init-credentials
  namespace: somenamespace
type: Opaque
---
# Create a secret to hold a keyfile used to authenticate between replicaset members
# this seems to need to be base64 encoded twice (might not be the case if this
# was an actual file reference as per the examples, but we're using a simple key
# here
apiVersion: v1
data:
  #echo -n "CHANGEMECHANGEMECHANGEME" | base64 | base64
  mongodb-keyfile: UTBoQlRrZEZUVVZEU0VGT1IwVk5SVU5JUVU1SFJVMUYK
kind: Secret
metadata:
  name: mongo-key
  namespace: somenamespace
type: Opaque
---
# Create a service account for Mongo and give it Pod List role
# note this is a ClusterROleBinding - the Mongo Pod will be able
# to list all pods present in the cluster regardless of namespace
# (and this is exactly what it does...see below)
apiVersion: v1
kind: ServiceAccount
metadata:
  name: mongo-serviceaccount
  namespace: somenamespace
---
apiVersion: rbac.authorization.k8s.io/v1
kind: ClusterRoleBinding
metadata:
  name: mongo-somenamespace-serviceaccount-view
  namespace: somenamespace
subjects:
- kind: ServiceAccount
  name: mongo-serviceaccount
  namespace: somenamespace
roleRef:
  apiGroup: rbac.authorization.k8s.io
  kind: ClusterRole
  name: pod-viewer
---
kind: ClusterRole
apiVersion: rbac.authorization.k8s.io/v1
metadata:
  name: pod-viewer
  namespace: somenamespace
rules:
- apiGroups: [""]
  resources: ["pods"]
  verbs: ["list"]
---
#Create a Storage Class for Google Container Engine
#Note fstype: xfs isn't supported by GCE yet and the
#Pod startup will hang if you try to specify it.
kind: StorageClass
apiVersion: storage.k8s.io/v1beta1
metadata:
  namespace: somenamespace
  name: mongodb-ssd-storage
provisioner: kubernetes.io/gce-pd
parameters:
  type: pd-ssd
allowVolumeExpansion: true
---
#Headless Service for StatefulSets
apiVersion: v1
kind: Service
metadata:
  namespace: somenamespace
  name: mongo-db
  labels:
    name: mongo-db
spec:
 ports:
 - port: 27017
   targetPort: 27017
 clusterIP: None
 selector:
   app: mongo
---
# Now the fun part
#
apiVersion: apps/v1beta1
kind: StatefulSet
metadata:
  namespace: somenamespace
  name: mongo-db
spec:
  serviceName: mongo-db
  replicas: 3
  template:
    metadata:
      labels:
        # Labels MUST match MONGO_SIDECAR_POD_LABELS
        # and MUST differentiate between other mongo
        # instances in the CLUSTER not just the namespace
        # as the sidecar will search the entire cluster
        # for something to configure
        app: mongo
        environment: somenamespace
    spec:
      #Run the Pod using the service account
      serviceAccountName: mongo-serviceaccount
      terminationGracePeriodSeconds: 10
      #Prevent a Mongo Replica running on the same node as another (avoid single point of failure)
      affinity:
        podAntiAffinity:
          requiredDuringSchedulingIgnoredDuringExecution:
          - labelSelector:
              matchExpressions:
              - key: app
                operator: In
                values:
                - mongo
            topologyKey: "kubernetes.io/hostname"
      containers:
        - name: mongo
          image: mongo:4.0.12
          command:
            #Authentication adapted from https://gist.github.com/thilinapiy/0c5abc2c0c28efe1bbe2165b0d8dc115
            #in order to pass the new admin user id and password in
          - /bin/sh
          - -c
          - >
            if [ -f /data/db/admin-user.lock ]; then
              echo "KUBERNETES LOG $HOSTNAME- Starting Mongo Daemon with runtime settings (clusterAuthMode)"
              #ensure wiredTigerCacheSize is set within the size of the containers memory limit
              mongod --wiredTigerCacheSizeGB 0.5 --replSet rs0 --bind_ip 0.0.0.0 --smallfiles --noprealloc --clusterAuthMode keyFile --keyFile /etc/secrets-volume/mongodb-keyfile --setParameter authenticationMechanisms=SCRAM-SHA-1;
            else
              echo "KUBERNETES LOG $HOSTNAME- Starting Mongo Daemon with setup setting (authMode)"
              mongod --auth;
            fi;
          lifecycle:
              postStart:
                exec:
                  command:
                  - /bin/sh
                  - -c
                  - >
                    if [ ! -f /data/db/admin-user.lock ]; then
                      echo "KUBERNETES LOG $HOSTNAME- no Admin-user.lock file found yet"
                      #replaced simple sleep, with ping and test.
                      while (! mongo --eval "db.adminCommand('ping')"); do sleep 10; echo "KUBERNETES LOG $HOSTNAME - waiting another 10 seconds for mongo to start" >> /data/db/configlog.txt; done;
                      touch /data/db/admin-user.lock
                      if [ "$HOSTNAME" = "mongo-db-0" ]; then
                        echo "KUBERNETES LOG $HOSTNAME- creating admin user ${MONGODB_USERNAME}"
                        mongo --eval "db = db.getSiblingDB('admin'); db.createUser({ user: '${MONGODB_USERNAME}', pwd: '${MONGODB_PASSWORD}', roles: [{ role: 'root', db: 'admin' }]});" >> /data/db/config.log
                      fi;
                      echo "KUBERNETES LOG $HOSTNAME-shutting mongod down for final restart"
                      mongod --shutdown;
                    fi;
          env:
            - name: MONGODB_USERNAME
              valueFrom:
                secretKeyRef:
                  name: mongo-init-credentials
                  key: init.userid
            - name: MONGODB_PASSWORD
              valueFrom:
                secretKeyRef:
                  name: mongo-init-credentials
                  key: init.password
          ports:
            - containerPort: 27017
          livenessProbe:
            exec:
              command:
              - mongo
              - --eval
              - "db.adminCommand('ping')"
            initialDelaySeconds: 5
            periodSeconds: 60
            timeoutSeconds: 10
          readinessProbe:
            exec:
              command:
              - mongo
              - --eval
              - "db.adminCommand('ping')"
            initialDelaySeconds: 5
            periodSeconds: 60
            timeoutSeconds: 10
          resources:
            requests:
              memory: "350Mi"
              cpu: 0.05
            limits:
              memory: "1Gi"
              cpu: 0.1
          volumeMounts:
            - name: mongo-key
              mountPath: "/etc/secrets-volume"
              readOnly: true
            - name: mongo-persistent-storage
              mountPath: /data/db
        - name: mongo-sidecar
          image: cvallance/mongo-k8s-sidecar
          env:
            # Sidecar searches for any POD in the CLUSTER with these labels
            # not just the namespace..so we need to ensure the POD is labelled
            # to differentiate it from other PODS in different namespaces
            - name: MONGO_SIDECAR_POD_LABELS
              value: "app=mongo,environment=somenamespace"
            - name: MONGODB_USERNAME
              valueFrom:
                secretKeyRef:
                  name: mongo-init-credentials
                  key: init.userid
            - name: MONGODB_PASSWORD
              valueFrom:
                secretKeyRef:
                  name: mongo-init-credentials
                  key: init.password
            #don't be fooled by this..it's not your DB that
            #needs specifying, it's the admin DB as that
            #is what you authenticate against with mongo.
            - name: MONGODB_DATABASE
              value: admin
      volumes:
      - name: mongo-key
        secret:
          defaultMode: 0400
          secretName: mongo-key
  volumeClaimTemplates:
  - metadata:
      name: mongo-persistent-storage
      annotations:
        volume.beta.kubernetes.io/storage-class: "mongodb-ssd-storage"
    spec:
      accessModes: [ "ReadWriteOnce" ]
      resources:
        requests:
          storage: 1Gi

Supposing you created a secret:

apiVersion: v1
kind: Secret
metadata:
  name: mysecret
type: Opaque
data:
  username: YWRtaW4=
  password: MWYyZDFlMmU2N2Rm

Here a snippet to get a value from a secret in a kubernetes yaml file:

 env:
      - name: MONGO_INITDB_ROOT_PASSWORD
        valueFrom:
          secretKeyRef:
            name: mysecret
            key: password