Aljoscha Krettek commented on BEAM-696:

Just to make it clear what the Flink runner does for this: When a GroupByKey 
has a merging {{WindowFn}} and side inputs we don't to any eager 
processing/merging of the inputs but defer until "as late as possible". This is 
essentially what [~pei...@gmail.com] mentioned for the data flow runner above.

> Side-Inputs non-deterministic with merging main-input windows
> -------------------------------------------------------------
>                 Key: BEAM-696
>                 URL: https://issues.apache.org/jira/browse/BEAM-696
>             Project: Beam
>          Issue Type: Bug
>          Components: beam-model
>            Reporter: Ben Chambers
>            Assignee: Pei He
> Side-Inputs are non-deterministic for several reasons:
> 1. Because they depend on triggering of the side-input (this is acceptable 
> because triggers are by their nature non-deterministic).
> 2. They depend on the current state of the main-input window in order to 
> lookup the side-input. This means that with merging
> 3. Any runner optimizations that affect when the side-input is looked up may 
> cause problems with either or both of these.
> This issue focuses on #2 -- the non-determinism of side-inputs that execute 
> within a Merging WindowFn.
> Possible solution would be to defer running anything that looks up the 
> side-input until we need to extract an output, and using the main-window at 
> that point. Specifically, if the main-window is a MergingWindowFn, don't 
> execute any kind of pre-combine, instead buffer all the inputs and combine 
> later.
> This could still run into some non-determinism if there are triggers 
> controlling when we extract output.

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