2

tl;dr

When starting a fresh percona cluster of 3 kubernetes pods, the grastate.dat seq_no is set at -1 and doesn't change. On deleting one pod and watching it restart, expecting it to rejoin the cluster, it sets it's inital position to 00000000-0000-0000-0000-000000000000:-1 and tries to connect to itself (it's former ip), maybe because it'd been the first pod in the cluster? It then timeouts in it's erroneous connection to itself:

2017-03-26T08:38:05.374058Z 0 [Note] WSREP: (b7571ff8, 'tcp://0.0.0.0:4567') connection to peer 00000000 with addr tcp://10.52.0.26:4567 timed out, no messages seen in PT3S

The cluster doesn't get started properly and I'm unable to successfully restart pods in the cluster.

Full

When I start the cluster from scratch. With blank data directories and a fresh etcd cluster, everything seems to come up. However I look at the grastate.dat and I find that the seq_no for each pod is -1:

root@gluster-3:/mnt/gfs/gluster_vol-1/mysql# cat percona-0/grastate.dat
# GALERA saved state
version: 2.1
uuid:    a91f70f2-11f8-11e7-8f3d-86c2e58790ac
seqno:   -1
safe_to_bootstrap: 0
root@gluster-3:/mnt/gfs/gluster_vol-1/mysql# cat percona-1/grastate.dat
# GALERA saved state
version: 2.1
uuid:    a91f70f2-11f8-11e7-8f3d-86c2e58790ac
seqno:   -1
safe_to_bootstrap: 0
root@gluster-3:/mnt/gfs/gluster_vol-1/mysql# cat percona-2/grastate.dat
# GALERA saved state
version: 2.1
uuid:    a91f70f2-11f8-11e7-8f3d-86c2e58790ac
seqno:   -1
safe_to_bootstrap: 0

At this point I can do mysql -h percona -u wordpress -p and connect and wordpress works too.

Scenario: I have 3 percona pods

/ # jonathan@ubuntu:~/Projects/k8wp$ kubectl get pods
NAME                         READY     STATUS    RESTARTS   AGE
etcd-0                       1/1       Running   1          12h
etcd-1                       1/1       Running   0          12h
etcd-2                       1/1       Running   3          12h
etcd-3                       1/1       Running   1          12h
percona-0                    1/1       Running   0          8m
percona-1                    1/1       Running   0          57m
percona-2                    1/1       Running   0          57m

When I try to restart percona-0 it gets kicked out of the cluster on restarting, percona-0's gvwstate.dat file shows

root@gluster-3:/mnt/gfs/gluster_vol-1/mysql# cat percona-0/gvwstate.dat
my_uuid: b7571ff8-11f8-11e7-bd2d-8b50487e1523
#vwbeg
view_id: 3 b7571ff8-11f8-11e7-bd2d-8b50487e1523 3
bootstrap: 0
member: b7571ff8-11f8-11e7-bd2d-8b50487e1523 0
member: bd05a643-11f8-11e7-9dab-1b4fc20eaf6a 0
member: c33d6a73-11f8-11e7-9e86-fe1cf3d3367a 0
#vwend

The other 2 pods in the cluster show:

root@gluster-3:/mnt/gfs/gluster_vol-1/mysql# cat percona-1/gvwstate.dat
my_uuid: bd05a643-11f8-11e7-9dab-1b4fc20eaf6a
#vwbeg
view_id: 3 bd05a643-11f8-11e7-9dab-1b4fc20eaf6a 4
bootstrap: 0
member: bd05a643-11f8-11e7-9dab-1b4fc20eaf6a 0
member: c33d6a73-11f8-11e7-9e86-fe1cf3d3367a 0
#vwend
root@gluster-3:/mnt/gfs/gluster_vol-1/mysql# cat percona-2/gvwstate.dat
my_uuid: c33d6a73-11f8-11e7-9e86-fe1cf3d3367a
#vwbeg
view_id: 3 bd05a643-11f8-11e7-9dab-1b4fc20eaf6a 4
bootstrap: 0
member: bd05a643-11f8-11e7-9dab-1b4fc20eaf6a 0
member: c33d6a73-11f8-11e7-9e86-fe1cf3d3367a 0
#vwend

Here are what I think are the relevant errors from percona-0's startup:

2017-03-26T08:37:58.370605Z 0 [Note] WSREP: Setting initial position to 00000000-0000-0000-0000-000000000000:-1
2017-03-26T08:37:58.372537Z 0 [Note] WSREP: gcomm: connecting to group 'wordpress-001', peer '10.52.0.26:'
2017-03-26T08:38:01.373345Z 0 [Note] WSREP: (b7571ff8, 'tcp://0.0.0.0:4567') connection to peer 00000000 with addr tcp://10.52.0.26:4567 timed out, no messages seen in PT3S
2017-03-26T08:38:01.373682Z 0 [Warning] WSREP: no nodes coming from prim view, prim not possible
2017-03-26T08:38:01.373750Z 0 [Note] WSREP: view(view_id(NON_PRIM,b7571ff8,5) memb {
    b7571ff8,0
} joined {
} left {
} partitioned {
})
2017-03-26T08:38:01.373838Z 0 [Note] WSREP: gcomm: connected
2017-03-26T08:38:01.373872Z 0 [Note] WSREP: Changing maximum packet size to 64500, resulting msg size: 32636
2017-03-26T08:38:01.373987Z 0 [Note] WSREP: Shifting CLOSED -> OPEN (TO: 0)
2017-03-26T08:38:01.374012Z 0 [Note] WSREP: Opened channel 'wordpress-001'
2017-03-26T08:38:01.374108Z 0 [Note] WSREP: Waiting for SST to complete.
2017-03-26T08:38:01.374417Z 0 [Note] WSREP: New COMPONENT: primary = no, bootstrap = no, my_idx = 0, memb_num = 1
2017-03-26T08:38:01.374469Z 0 [Note] WSREP: Flow-control interval: [16, 16]
2017-03-26T08:38:01.374491Z 0 [Note] WSREP: Received NON-PRIMARY.
2017-03-26T08:38:01.374560Z 1 [Note] WSREP: New cluster view: global state: :-1, view# -1: non-Primary, number of nodes: 1, my index: 0, protocol version -1

The ip it's trying to connect to 10.52.0.26 in 2017-03-26T08:37:58.372537Z 0 [Note] WSREP: gcomm: connecting to group 'wordpress-001', peer '10.52.0.26:' is actually that pods previous ip, here's the listing of keys in etcd I did before deleting percona-0

/ # etcdctl ls --recursive
/pxc-cluster
/pxc-cluster/wordpress
/pxc-cluster/queue
/pxc-cluster/queue/wordpress
/pxc-cluster/queue/wordpress-001
/pxc-cluster/wordpress-001
/pxc-cluster/wordpress-001/10.52.1.46
/pxc-cluster/wordpress-001/10.52.1.46/ipaddr
/pxc-cluster/wordpress-001/10.52.1.46/hostname
/pxc-cluster/wordpress-001/10.52.2.33
/pxc-cluster/wordpress-001/10.52.2.33/ipaddr
/pxc-cluster/wordpress-001/10.52.2.33/hostname
/pxc-cluster/wordpress-001/10.52.0.26
/pxc-cluster/wordpress-001/10.52.0.26/hostname
/pxc-cluster/wordpress-001/10.52.0.26/ipaddr

After kubectl delete pods/percona-0:

/ # etcdctl ls --recursive
/pxc-cluster
/pxc-cluster/queue
/pxc-cluster/queue/wordpress
/pxc-cluster/queue/wordpress-001
/pxc-cluster/wordpress-001
/pxc-cluster/wordpress-001/10.52.1.46
/pxc-cluster/wordpress-001/10.52.1.46/ipaddr
/pxc-cluster/wordpress-001/10.52.1.46/hostname
/pxc-cluster/wordpress-001/10.52.2.33
/pxc-cluster/wordpress-001/10.52.2.33/ipaddr
/pxc-cluster/wordpress-001/10.52.2.33/hostname
/pxc-cluster/wordpress

Also during the restart percona-0 tried to register to etcd with:

{"action":"create","node":{"key":"/pxc-cluster/queue/wordpress-001/00000000000000009886","value":"10.52.0.27","expiration":"2017-03-26T08:38:57.980325718Z","ttl":60,"modifiedIndex":9886,"createdIndex":9886}}
{"action":"set","node":{"key":"/pxc-cluster/wordpress-001/10.52.0.27/ipaddr","value":"10.52.0.27","expiration":"2017-03-26T08:38:28.01814818Z","ttl":30,"modifiedIndex":9887,"createdIndex":9887}}
{"action":"set","node":{"key":"/pxc-cluster/wordpress-001/10.52.0.27/hostname","value":"percona-0","expiration":"2017-03-26T08:38:28.037188157Z","ttl":30,"modifiedIndex":9888,"createdIndex":9888}}
{"action":"update","node":{"key":"/pxc-cluster/wordpress-001/10.52.0.27","dir":true,"expiration":"2017-03-26T08:38:28.054726795Z","ttl":30,"modifiedIndex":9889,"createdIndex":9887},"prevNode":{"key":"/pxc-cluster/wordpress-001/10.52.0.27","dir":true,"modifiedIndex":9887,"createdIndex":9887}}

which doesn't work.

From the second member of the cluster percona-1:

2017-03-26T08:37:44.069583Z 0 [Note] WSREP: (bd05a643, 'tcp://0.0.0.0:4567') turning message relay requesting on, nonlive peers: tcp://10.52.0.26:4567 
2017-03-26T08:37:45.069756Z 0 [Note] WSREP: (bd05a643, 'tcp://0.0.0.0:4567') reconnecting to b7571ff8 (tcp://10.52.0.26:4567), attempt 0
2017-03-26T08:37:48.570332Z 0 [Note] WSREP: (bd05a643, 'tcp://0.0.0.0:4567') connection to peer 00000000 with addr tcp://10.52.0.26:4567 timed out, no messages seen in PT3S
2017-03-26T08:37:49.605089Z 0 [Note] WSREP: evs::proto(bd05a643, GATHER, view_id(REG,b7571ff8,3)) suspecting node: b7571ff8
2017-03-26T08:37:49.605276Z 0 [Note] WSREP: evs::proto(bd05a643, GATHER, view_id(REG,b7571ff8,3)) suspected node without join message, declaring inactive
2017-03-26T08:37:50.104676Z 0 [Note] WSREP: declaring c33d6a73 at tcp://10.52.2.33:4567 stable

New Info: I restarted percona-0 again, and this time it somehow came up! After a few tries I realised the pod needs to restarted twice to come up i.e. after deleting it the first time, it comes up with the above errors, after deleting it the second time it comes up okay and syncs with the other members. Could this be because it was the first pod in the cluster?

I've tested deleting the other pods but they all come back up okay.

The issue only lies with percona-0.

Also; Taking down all the pods at once, if my node was to crash, that's the situation where the pods don't come back up at all! I suspect it's because no state is saved to grastate.dat , i.e. seq_no remains -1 even though the global id may change, the pods exit with mysqld shutdown, and the following errors:

jonathan@ubuntu:~/Projects/k8wp$ kubectl logs percona-2 | grep ERROR
2017-03-26T11:20:25.795085Z 0 [ERROR] WSREP: failed to open gcomm backend connection: 110: failed to reach primary view: 110 (Connection timed out)
2017-03-26T11:20:25.795276Z 0 [ERROR] WSREP: gcs/src/gcs_core.cpp:gcs_core_open():208: Failed to open backend connection: -110 (Connection timed out)
2017-03-26T11:20:25.795544Z 0 [ERROR] WSREP: gcs/src/gcs.cpp:gcs_open():1437: Failed to open channel 'wordpress-001' at 'gcomm://10.52.2.36': -110 (Connection timed out)
2017-03-26T11:20:25.795618Z 0 [ERROR] WSREP: gcs connect failed: Connection timed out
2017-03-26T11:20:25.795645Z 0 [ERROR] WSREP: wsrep::connect(gcomm://10.52.2.36) failed: 7
2017-03-26T11:20:25.795693Z 0 [ERROR] Aborting
jonathan@ubuntu:~/Projects/k8wp$ kubectl logs percona-1 | grep ERROR
2017-03-26T11:20:27.093780Z 0 [ERROR] WSREP: failed to open gcomm backend connection: 110: failed to reach primary view: 110 (Connection timed out)
2017-03-26T11:20:27.093977Z 0 [ERROR] WSREP: gcs/src/gcs_core.cpp:gcs_core_open():208: Failed to open backend connection: -110 (Connection timed out)
2017-03-26T11:20:27.094145Z 0 [ERROR] WSREP: gcs/src/gcs.cpp:gcs_open():1437: Failed to open channel 'wordpress-001' at 'gcomm://10.52.1.49': -110 (Connection timed out)
2017-03-26T11:20:27.094200Z 0 [ERROR] WSREP: gcs connect failed: Connection timed out
2017-03-26T11:20:27.094227Z 0 [ERROR] WSREP: wsrep::connect(gcomm://10.52.1.49) failed: 7
2017-03-26T11:20:27.094247Z 0 [ERROR] Aborting
jonathan@ubuntu:~/Projects/k8wp$ kubectl logs percona-0 | grep ERROR
2017-03-26T11:20:52.040214Z 0 [ERROR] WSREP: failed to open gcomm backend connection: 110: failed to reach primary view: 110 (Connection timed out)
2017-03-26T11:20:52.040279Z 0 [ERROR] WSREP: gcs/src/gcs_core.cpp:gcs_core_open():208: Failed to open backend connection: -110 (Connection timed out)
2017-03-26T11:20:52.040385Z 0 [ERROR] WSREP: gcs/src/gcs.cpp:gcs_open():1437: Failed to open channel 'wordpress-001' at 'gcomm://10.52.2.36': -110 (Connection timed out)
2017-03-26T11:20:52.040437Z 0 [ERROR] WSREP: gcs connect failed: Connection timed out
2017-03-26T11:20:52.040471Z 0 [ERROR] WSREP: wsrep::connect(gcomm://10.52.2.36) failed: 7
2017-03-26T11:20:52.040508Z 0 [ERROR] Aborting

grastate.dat on deleting all pods:

root@gluster-3:/mnt/gfs/gluster_vol-1/mysql# cat percona-0/grastate.dat
# GALERA saved state
version: 2.1
uuid:    a91f70f2-11f8-11e7-8f3d-86c2e58790ac
seqno:   -1
safe_to_bootstrap: 0
 root@gluster-3:/mnt/gfs/gluster_vol-1/mysql# cat percona-1/grastate.dat
# GALERA saved state
version: 2.1
uuid:    a91f70f2-11f8-11e7-8f3d-86c2e58790ac
seqno:   -1
safe_to_bootstrap: 0
 root@gluster-3:/mnt/gfs/gluster_vol-1/mysql# cat percona-2/grastate.dat
# GALERA saved state
version: 2.1
uuid:    a91f70f2-11f8-11e7-8f3d-86c2e58790ac
seqno:   -1
safe_to_bootstrap: 0

No, gvwstate.dat

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1 Answer 1

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Fixed it with changing the entrypoint in the container to the following script:

#!/bin/bash
sed -i \"s|safe_to_bootstrap.*:.*|safe_to_bootstrap:1|1\" /var/lib/mysql/grastate.dat; 
/entrypoint.sh --wsrep-new-cluster;

Thanks to https://www.claudiokuenzler.com/blog/494/galera-cluster-mysql-not-starting-failed-to-open-channel-reach-primary#.WNesDiF97Qo

The issue is, when restarting the 3 pods from a crash, they all hit the following error:

[ERROR] WSREP: failed to open gcomm backend connection: 110: failed to reach primary view: 110 (Connection timed out)

What that means (summarizing from the the link), is that since all the pods are down the first pod (the pods are managed by a statefulset) comes up and tries to reconnect to the cluster but doesn't find any other pods it can connect to, so it goes down, the next pod comes up tries the same thing, hits the same error and goes down to etc etc

The solution is for the first pod to start a new cluster when it comes up then all the subsequent will come up and find a node to connect to. It'll still come up with all the data.

So with percona xtradb the docker container's entrypoint looks like:

exec mysqld --user=mysql --wsrep_cluster_name=$CLUSTER_NAME --wsrep_cluster_address="gcomm://$cluster_join" --wsrep_sst_method=xtrabackup-v2 --wsrep_sst_auth="xtrabackup:$XTRABACKUP_PASSWORD" --log-error=${DATADIR}error.log $CMDARG

So all I have to do to get the setup running is pass the earlier argument --wsrep-new-cluster to the /entrypoint.sh file like so:

/entrypoint.sh --wsrep-new-cluster

PS// I tried the above at first alone but I ran into an error stating that to force a new cluster and bootstrap with that node I had to set safe_to_bootstrap from 0 to 1 in /var/lib/mysql/grastate.dat

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