Running mongo with persistent volume throws error - Kubernetes

2
votes

Context

I'd like to create a mongodb stateful deployment that shares my host's local directory /mnt/nfs/data/myproject/production/permastore/mogno (network file system directory) with all mongodb pods at /data/db. I'm running my kubernetes cluster on three VirtualMachines.

Problem

When I don't use persistent volume claims I can start mongo without any problem! But, when I start mongodb with persistent volume claim, I get this error.

Error: couldn't connect to server 127.0.0.1:27017, connection attempt failed: SocketException: Error connecting to 127.0.0.1:27017 :: caused by :: Connection refused :

Question

Does anyone know why mongo fails to start, when /data/db is mountend with persistent volume? How to fix it?

Code

Below config files will not work in your environment due to differents paths. However, you should be able to get idea behind my setup.

Persistent Volume pv.yaml

apiVersion: v1
kind: PersistentVolume
metadata:
  name: phenex-mongo
  labels:
    type: local
spec:
  accessModes:
  - ReadWriteOnce
  capacity:
    storage: 1Gi
  hostPath:
    path: /mnt/nfs/data/phenex/production/permastore/mongo
  claimRef:
    name: phenex-mongo
  persistentVolumeReclaimPolicy: Retain
  storageClassName: manual
  volumeMode: Filesystem

Persistent Volume Claim pvc.yaml

apiVersion: v1
kind: PersistentVolumeClaim
metadata:
  name: phenex-mongo
spec:
  storageClassName: manual
  accessModes:
    - ReadWriteOnce
  resources:
    requests:
      storage: 100Mi

Deployment deployment.yaml

apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  name: mongo
  labels:
    run: mongo
spec:
  selector:
    matchLabels:
      run: mongo
  strategy:
    type: Recreate
  template:
    metadata:
      labels:
        run: mongo
    spec:
      containers:
      - image: mongo:4.2.0-bionic
        name: mongo
        ports:
        - containerPort: 27017
          name: mongo
         volumeMounts:
         - name: phenex-mongo
           mountPath: /data/db
       volumes:
       - name: phenex-mongo
         persistentVolumeClaim:
           claimName: phenex-mongo

Applying configs

$ kubectl apply -f pv.yaml
$ kubectl apply -f pc.yaml
$ kubectl apply -f deployment.yaml

Checking cluster state

$ kubectl get deploy,po,pv,pvc --output=wide
NAME                          READY   UP-TO-DATE   AVAILABLE   AGE   CONTAINERS   IMAGES               SELECTOR
deployment.extensions/mongo   1/1     1            1           38m   mongo        mongo:4.2.0-bionic   run=mongo

NAME                         READY   STATUS    RESTARTS   AGE   IP          NODE    NOMINATED NODE   READINESS GATES
pod/mongo-59f669657d-fpkgv   1/1     Running   0          35m   10.44.0.2   web01   <none>           <none>

NAME                            CAPACITY   ACCESS MODES   RECLAIM POLICY   STATUS   CLAIM                 STORAGECLASS   REASON   AGE    VOLUMEMODE
persistentvolume/phenex-mongo   1Gi        RWO            Retain           Bound    phenex/phenex-mongo   manual                  124m   Filesystem

NAME                                 STATUS   VOLUME         CAPACITY   ACCESS MODES   STORAGECLASS   AGE    VOLUMEMODE
persistentvolumeclaim/phenex-mongo   Bound    phenex-mongo   1Gi        RWO            manual         122m   Filesystem

Running mongo pod

$ kubectl exec -it mongo-59f669657d-fpkgv mongo
MongoDB shell version v4.2.0
connecting to: mongodb://127.0.0.1:27017/?compressors=disabled&gssapiServiceName=mongodb
2019-08-14T14:25:25.452+0000 E  QUERY    [js] Error: couldn't connect to server 127.0.0.1:27017, connection attempt failed: SocketException: Error connecting to 127.0.0.1:27017 :: caused by :: Connection refused :
connect@src/mongo/shell/mongo.js:341:17
@(connect):2:6
2019-08-14T14:25:25.453+0000 F  -        [main] exception: connect failed
2019-08-14T14:25:25.453+0000 E  -        [main] exiting with code 1
command terminated with exit code 1

Logs

$ kubectl logs mongo-59f669657d-fpkgv 
2019-08-14T14:00:32.287+0000 I  CONTROL  [main] Automatically disabling TLS 1.0, to force-enable TLS 1.0 specify --sslDisabledProtocols 'none'
2019-08-14T14:00:32.291+0000 I  CONTROL  [initandlisten] MongoDB starting : pid=1 port=27017 dbpath=/data/db 64-bit host=mongo-59f669657d-fpkgv
2019-08-14T14:00:32.291+0000 I  CONTROL  [initandlisten] db version v4.2.0
2019-08-14T14:00:32.291+0000 I  CONTROL  [initandlisten] git version: a4b751dcf51dd249c5865812b390cfd1c0129c30
2019-08-14T14:00:32.291+0000 I  CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.1.1  11 Sep 2018
2019-08-14T14:00:32.291+0000 I  CONTROL  [initandlisten] allocator: tcmalloc
2019-08-14T14:00:32.291+0000 I  CONTROL  [initandlisten] modules: none
2019-08-14T14:00:32.291+0000 I  CONTROL  [initandlisten] build environment:
2019-08-14T14:00:32.291+0000 I  CONTROL  [initandlisten]     distmod: ubuntu1804
2019-08-14T14:00:32.291+0000 I  CONTROL  [initandlisten]     distarch: x86_64
2019-08-14T14:00:32.291+0000 I  CONTROL  [initandlisten]     target_arch: x86_64
2019-08-14T14:00:32.291+0000 I  CONTROL  [initandlisten] options: { net: { bindIp: "*" } }

root@mongo-59f669657d-fpkgv:/# ps aux
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
mongodb      1  0.0  2.7 208324 27920 ?        Dsl  14:00   0:00 mongod --bind_ip_all
root        67  0.0  0.2  18496  2060 pts/1    Ss   15:12   0:00 bash
root        81  0.0  0.1  34388  1536 pts/1    R+   15:13   0:00 ps aux
1
mongodbkubernetes
Please add kubectl logs -l run=mongo – FL3SH
kubectl exec -it mongo-59f669657d-fpkgv -- ps aux please add it also – FL3SH
I need the whole line so run ps aux inside pod. – FL3SH
@FL3SH only three processes are running. I updated the logging section – Lukasz Dynowski
Let us continue this discussion in chat. – Lukasz Dynowski

1 Answers

2
votes

I've found cause and solution! In my setup, I was sharing a directory over a network using NFS. This way, all my cluster nodes (minions) had access to common directory located at /mnt/nfs/data/.

Cause

The reason that mongo couldn't start was due to invalid Persistent Volumes. Namely, I was using persistent volume HostPath type - this will work for a single node testing, or if you manually create directory structure on all your cluster nodes e.g. /tmp/your_pod_data_dir/. But, if you will try to mount nfs directory as a hostPath it will cause problems -such I had!

Solution

For directories that are shared over Network File System use NFS persistent volume type (NFS Example)! Below you will find my setup and two solutions.

Setup

/etc/hosts - my cluster nodes.

# Cluster nodes
192.168.123.130 master
192.168.123.131 web01
192.168.123.132 compute01
192.168.123.133 compute02

List of exported NFS directories.

[vagrant@master]$ showmount -e
Export list for master:
/nfs/data compute*,web*
/nfs/www  compute*,web*

First solution

This solution, shows deployment that mounts nfs directory via volumes -have a look at volumes and volumeMounts section.

apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  name: mongo
  labels:
    run: mongo
spec:
  selector:
    matchLabels:
      run: mongo
  strategy:
    type: Recreate
  template:
    metadata:
      labels:
        run: mongo
    spec:
      containers:
      - image: mongo:4.2.0-bionic
        name: mongo
        ports:
        - containerPort: 27017
          name: mongo
        volumeMounts:
        - name: phenex-nfs
          mountPath: /data/db
      volumes:
      - name: phenex-nfs
        nfs:
          # IP of master node
          server: 192.168.123.130
          path: /nfs/data/phenex/production/permastore/mongo

Second solution

This solution, shows deployment that mounts nfs directory via volume claims -have a look at persistentVolumeClaim, Persistent Volume and Persistent Volume Claim are defined below.

apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  name: mongo
  labels:
    run: mongo
spec:
  selector:
    matchLabels:
      run: mongo
  strategy:
    type: Recreate
  template:
    metadata:
      labels:
        run: mongo
    spec:
      containers:
      - image: mongo:4.2.0-bionic
        name: mongo
        ports:
        - containerPort: 27017
          name: mongo
        volumeMounts:
        - name: phenex-nfs
          mountPath: /data/db
      volumes:
      - name: phenex-nfs
        persistentVolumeClaim:
          claimName: phenex-nfs

Persistent Volume - NFS

apiVersion: v1
kind: PersistentVolume
metadata:
  name: phenex-nfs
spec:
  accessModes:
  - ReadWriteOnce
  capacity:
    storage: 1Gi
  nfs:
    # IP of master node
    server: 192.168.123.130
    path: /nfs/data
  claimRef:
    name: phenex-nfs
  persistentVolumeReclaimPolicy: Retain

Persistent Volume Claim

apiVersion: v1
kind: PersistentVolumeClaim
metadata:
  name: phenex-nfs
spec:
  accessModes:
    - ReadWriteOnce
  resources:
    requests:
      storage: 100Mi

Expected Output

# Checking cluster state
[vagrant@master ~]$ kubectl get deploy,po,pv,pvc --output=wide
NAME                          READY   UP-TO-DATE   AVAILABLE   AGE   CONTAINERS   IMAGES               SELECTOR
deployment.extensions/mongo   1/1     1            1           18s   mongo        mongo:4.2.0-bionic   run=mongo

NAME                         READY   STATUS    RESTARTS   AGE   IP          NODE    NOMINATED NODE   READINESS GATES
pod/mongo-65b7d6fb9f-mcmvj   1/1     Running   0          18s   10.44.0.2   web01   <none>           <none>

NAME                            CAPACITY   ACCESS MODES   RECLAIM POLICY   STATUS   CLAIM                 STORAGECLASS   REASON   AGE     VOLUMEMODE
persistentvolume/phenex-nfs     1Gi        RWO            Retain           Bound    /phenex-nfs                             27s     Filesystem

NAME                                 STATUS   VOLUME         CAPACITY   ACCESS MODES   STORAGECLASS   AGE     VOLUMEMODE
persistentvolumeclaim/phenex-nfs     Bound    phenex-nfs     1Gi        RWO                           27s     Filesystem

# Attaching to pod and checking network bindings
[vagrant@master ~]$ kubectl exec -it mongo-65b7d6fb9f-mcmvj -- bash
root@mongo-65b7d6fb9f-mcmvj:/$ apt update
root@mongo-65b7d6fb9f-mcmvj:/$ apt install net-tools
root@mongo-65b7d6fb9f-mcmvj:/$ netstat -tunlp tcp 0 0 0.0.0.0:27017
Active Internet connections (only servers)
Proto Recv-Q Send-Q Local Address           Foreign Address         State       PID/Program name    
tcp        0      0 0.0.0.0:27017           0.0.0.0:*               LISTEN      - 

# Running mongo clinet
root@mongo-65b7d6fb9f-mcmvj:/$ mongo
MongoDB shell version v4.2.0
connecting to: mongodb://127.0.0.1:27017/?compressors=disabled&gssapiServiceName=mongodb
Implicit session: session { "id" : UUID("45287a0e-7d41-4484-a267-5101bd20fad3") }
MongoDB server version: 4.2.0
Server has startup warnings: 
2019-08-14T18:03:29.703+0000 I  CONTROL  [initandlisten] 
2019-08-14T18:03:29.703+0000 I  CONTROL  [initandlisten] ** WARNING: Access control is not enabled for the database.
2019-08-14T18:03:29.703+0000 I  CONTROL  [initandlisten] **          Read and write access to data and configuration is unrestricted.
2019-08-14T18:03:29.703+0000 I  CONTROL  [initandlisten] 
2019-08-14T18:03:29.703+0000 I  CONTROL  [initandlisten] 
2019-08-14T18:03:29.703+0000 I  CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/enabled is 'always'.
2019-08-14T18:03:29.703+0000 I  CONTROL  [initandlisten] **        We suggest setting it to 'never'
2019-08-14T18:03:29.703+0000 I  CONTROL  [initandlisten] 
2019-08-14T18:03:29.703+0000 I  CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/defrag is 'always'.
2019-08-14T18:03:29.703+0000 I  CONTROL  [initandlisten] **        We suggest setting it to 'never'
2019-08-14T18:03:29.703+0000 I  CONTROL  [initandlisten] 
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