Restart Mongodb with not enough nodes in a replica set

The context could be a virtualised cluster, where an hypervisor went suddenly down. 2 of your Mongo replicas are unavailable, only 1 is left, which then of course drops back to being secondary and read only.

You want to have this server running alone for a while while the others come back online, as you decide that it is better to have potential small inconsistency instead of not running for a few hours. The thing is that this last server will complain that the rest of the set is not available. To get it started again, you just need to make it forget about the rest of the set.

  1. Switch the service off
    service mongodb stop
  2. Remove the line replSet from your /etc/mongodb.conf
  3. Restart the service
    service mongodb start

    Mongo will complain:

    mongod started without --replSet yet 1 documents are present in local.system.replset
     [initandlisten] ** Restart with --replSet unless you are doing maintenance and no other clients are connected.
     [initandlisten] ** The TTL collection monitor will not start because of this.
     [initandlisten] ** For more info see
  4. Remove the offending document in system.replset from the mongoshell
    // will give you one document back
    // remove all documents (there is only one)
    // check resultset is empty
  5. Restart mongo
    service mongodb stop
    service mongodb start
  6. Once the other nodes are up, add again the replSet line in /etc/mongodb.conf and restart the service.

Replacing a single mongoDB server

I am moving a single mongoDB server to another hardware, and I want to do that with the least possible production interruption, of course.

Well, it so happens that it is not possible if you did not plan it from the start. You can argue that if I have a single SPOF server in production I am doing my job badly, but this is beside the point for this post.

MongoDB has this neat replication features, where you can build a cluster of servers, with one primary and a few slaves (secondaries), among other options. If you properly configured mongo to use this feature, then you can add a secondary, promote it to primary to eventually switch off the initial primary. This is what I will describe here.

Note that there will be 2 (very short) downtimes. One to create a replica set (this is just a restart), and one where the primaries are switched (you need to redirect connections to your new primary).

A note about vagrant

If you are using vagrant, make sure that you use the plugin vagrant-hostmanager (vagrant plugin install vagrant-hostmanager) which helps managing /etc/hosts from inside vagrant boxes. Furthermore, make sure you set a different hostname to each of your VMs. By default, if you use the same basebox, they will probably end up having the same hostname (config.vm.hostname in your vagrant file, or the more specific version if you define a cluster inside your vagrantfile).

Configure the replication set

First of all, you need to tell mongoDB to use the replication feature. If not you will end up with messages like:

> rs.initiate()
{ "ok" : 0, "errmsg" : "server is not running with --replSet" }

You just need to update your /etc/mongodb.conf to add a line like so:


This is the config option that enables the replication. All servers in your replica set will have the same option, with the same value.

On a side note, in the same file make sure you are not binding only to, or you will have trouble having your 2 mongo instances talking to each other.

The sad thing is that mongo cannot reload its config file:

root@debian-800-jessie:~# service mongodb reload
[warn] Reloading mongodb daemon: not implemented, as the daemon ... (warning).
[warn] cannot re-read the config file (use restart). ... (warning).

Right. So a restart is needed:

service mongodb restart

You can now connect to your mongo shell the usual way, and initialise the replica set. This follows part of the tutorial explaining how to convert a standalone server to a replica set. Just type in the mongo shell:


and the (1 machine) replica set is now operational.

You can check this easily:

> rs.conf()
  "_id" : "spof",
  "version" : 1,
  "members" : [
  "_id" : 0,
  "host" : "debian-800-jessie:27017"

On your (new with an empty mongo) server, make sure that you add the replSet line as well in mongodb.conf.

Note that the hostname must be resolvable on the other machine of the cluster. If mongoDB somehow picked the local hostname, your replica set will just not work. If the local hostname has been picked up, see option 2 (reconfig) below.

You are now ready to add the second server to the set.

spof:PRIMARY> rs.add("")
{ "ok" : 1 }

We can check that all is fine:

spof:PRIMARY> rs.conf()
   "_id" : "spof",
   "version" : 3,
   "members" : [
       "_id" : 0,
       "host" : "debian-800-jessie:27017"
       "_id" : 1,
       "host" : ""

If the local hostname was chosen, the easiest option is to fully reconfigure the replica set from within the mongo shell, based on your current configuration :

// Get current configuration object
// update the current machine to use the non local name
// fully add server 2
cfg.members[1]={"_id":1, host:""}
// use this new config

Ok, we are all good, and the replica set is properly set up. What happened on our server2 which was empty when we started?

on server2:

spof:SECONDARY> use events
error: { "$err" : "not master and slaveOk=false", "code" : 13435 }

Hum, what does that mean? In short, there is a replication delay between the primary and secondary, so by default mongo disables reads to the secondary to make sure you always read up to date data. You can read more about read preferences, but to tell mongo that yes, you know what you are doing, just issue the slaveOK() command:

spof:SECONDARY> rs.slaveOk()
{ "_id" : ObjectId("556d550b59a5fb8615044c72"), "name" : "relevant" }

Success! (In this vagrant example, there was only one document in the collection).

In real life, if the secondary needs to sync a lot of data, it will stay in state STARTUP2 for a long time, which you can see via rs.status(). In the log files of the new secondary, you can see progress per collections. It will then move to RECOVERING to finally become SECONDARY, which is when it will start accepting connections.

Switch primaries

We are all set, you waited long enough to have the secondary in sync with the primary. What now? We first need to switch primary and secondary roles. This can be done easily by changing the priorities:

spof:PRIMARY> cfg=rs.conf()
spof:PRIMARY> cfg.members[0].priority=0.5
spof:PRIMARY> cfg.members[1].priority=1
spof:PRIMARY> rs.reconfig(cfg)

As you can see, your prompt changed from primary to secondary.

From this moment on, all connections to your now secondary should succeed but you will not be able to do much (secondary cannot write, and remember slaveOk()). You must thus be sure that your client connect to the new primary, or that you know that the connection is readonly in which case you can use slaveOk(). This switchover will be your last downtime.

Clean up

you can tell your new master that the secondary is not needed anymore:


Note that if you switch the secondary off (service mongodb stop), then the primary will step down to secondary as well, as it cannot guarantee that it is in a coherent state. This is what you get from using a replica set with only 2 machines.

You can now dispose of your old primary as you wish.

If you want to play around with your old primary, you will be out of luck to start with:

"not master or secondary; cannot currently read from this replSet member"

It will of course be obvious that you need to remove the replSet value from mongodb.conf and restart the server. Sadly, you will then be greeted by another, longer message when you connect:

Server has startup warnings: 
Wed Jun 3 13:10:44.435 [initandlisten] 
Wed Jun 3 13:10:44.435 [initandlisten] ** WARNING: mongod started without --replSet yet 1 documents are present in local.system.replset
Wed Jun 3 13:10:44.435 [initandlisten] ** Restart with --replSet unless you are doing maintenance and no other clients are connected.
Wed Jun 3 13:10:44.435 [initandlisten] ** The TTL collection monitor will not start because of this.
Wed Jun 3 13:10:44.435 [initandlisten] ** For more info see
Wed Jun 3 13:10:44.435 [initandlisten]

Well, the solution is almost obvious from the error message. If there is a document in local.system.replset, let’s just remove it!

> use local
switched to db local
> db.system.replset.find()
{ "_id" : "spof", "version" : 4, "members" : [ { "_id" : 1, "host" : "" } ] }
> db.system.replset.remove()
> db.system.replset.find()

Once you exit and reconnect to mongoDB, all will be fine, and will have your nice standalone server back.