Thanks for the answer.

Changing the mongodb params came from earlier posts on the forum
https://community.nodebb.org/topic/10810/connection-to-mongodb-that-is-hosted-on-atlas/6

I take that I could as well include them directly in the config.sjon as parameters to the uri query.

Yes, I did spend hours on googling this and similar error messages.

No, you can't create any collection manually on admin on MongoDb Atlas.
Neither from CLI nor from web interface.
Have upgraded from M0 to M2 just to see if there would be any impact but it isn't.

The most interesting thing is that the collection socket.io on admin was not created on local instance in order to get the nodebb to run. I am able to create it locally but setup did not create it.

Setting up a cluster on Atlas Mongodb.

My config

{
    "url": "http://localhost:4567",
    "secret": "dc0b3fff-4312-1234-4321-e5a327824225",
    "database": "mongo",
    "port": "4567",
    "mongo": {
        "host": "cluster0-shard-00-00-z1243.mongodb.net,cluster0-shard-00-01-z1234.mongodb.net,cluster0-shard-00-02-z1234.mongodb.net",
        "port": "27017,27017,27017",
        "username": "dbUser",
        "password": "1234123412341234",
        "database": "somedbname",
        "uri": "mongodb+srv://dbUser:[email protected]/somedbname?retryWrites=true"
    }
}

Changes in the mongo.js file

ssl: true,
authSource: 'admin',
replicaSet: 'Cluster0-shard-0',

I can successfully complete the .\nodebb setup command.
It also works as expected against local instance of Mongodb but when I run it against Atlas cluster I get:

not authorized on admin to execute command { create: "socket.io", capped: true, size: 5242880 }"

I can successfully connect and work with a local instance of mongodb.
However, when from local dev machine I change the mongodb connection string to point to Mongodb Atlas I get the following error:

not authorized on admin to execute command { create: "socket.io", capped: true, size: 5242880 } {"name":"MongoError","ok":0,"errmsg":"not authorized on admin to execute command { create: \"socket.io\", capped: true, size: 5242880 }","code":8000,"codeName":"AtlasError"}

The database is hosted on Mongodb Atlas cluster.

The user is assigned a role: atlasAdmin @ admin.

{
    "url": "http://localhost:4567",
    "secret": "somesecret",
    "database": "mongo",
    "mongo": {
        "host": "127.0.0.1",
        "port": 27017,
        "username": "",
        "password": "",
        "database": "",
        "uri": "mongodb+srv://<user>:<password>@somecluster.mongodb.net/somedbname"
    },
    "port": "4567"
}

MongoDb npm package version: 3.2.3

MongoDb version on Atlas: 4.0.8