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I am connecting clients to our servers using SignalR (same as socketio websockets) so I can send them notifications for activities in the system. It is NOT a chat application. So messages when sent will be for a particular user only.

These clients are connected on multiple web servers and these servers are subscribed to a redis backplane. Like mentioned in this article - http://www.asp.net/signalr/overview/performance/scaleout-in-signalr

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My question here is for this kind of notification system, in redis pubsub - should i have multiple channels - one per user in the backplane and the app server listening to each users notification channel. Or have one channel for all these notifications and the app server parses each message and figure out if they have that userid connected and send the message to that user.

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Based on the little I know about the details of your application, I think you should create channels/lists in the backplane/Redis on a per-client basis. This would be cheap in Redis, and it gives the server side process handling a specific client only the notifications they are supposed to have.

This should save your application iteration or handling of irrelevant data, which could have implications of performance at scale, and if security is at all a concern (don't know what the domain or application is), then it would be best to never retrieve/receive information unnecessarily that wasn't intended for a particular client.

I will pose a final question and some thoughts which I think support my opinion. If you don't do this on a client-by-client basis, then how will you handle when the user is not present to receive a message? You would either have to throw that message away, or have the application server handle that un-received message for every single client, every time they poll or otherwise receive information from Redis. This could really add up. Although, without knowing the details of the application, I'm not sure if this paragraph is relevant.

At the end of the day, though approaches and opinions may vary depending on the application, I would think about the architecture in terms of the entities and you outlined. You have clients, and they send and receive messages directly to one another. Those messages should be associated with each of the parties involved somehow, and they should be stored in a manner that will be efficient for lookup and which helps define/outline the structure of the application.

Hope my 2c helps!