We are planning to work on this clean shut down after releasing Flink 1.4. 
Implementing this properly would require some work, for example:
- adding some checkpoint options to add information about “closing”/“shutting 
down” event
- add clean shutdown to source functions API
- implement handling of this clean shutdown in desired sources

Those are not super complicated changes but also not trivial.

One thing that you could do, is to implement some super hacky filter function 
just after source operator, that you would manually trigger. Normally it would 
pass all of the messages. Once triggered, it would wait for next checkpoint to 
happen. It would assume that it is a save point, and would start filtering out 
all of the subsequent messages. When this checkpoint completes, you could 
manually shutdown your Flink application. This could guarantee that there are 
no duplicated writes after a restart. This might work for clean shutdown, but 
it would be a very hacky solution. 

Btw, keep in mind that even with clean shutdown you can end up with duplicated 
messages after a crash and there is no way around this with Kafka 0.9.

Piotrek

> On Oct 2, 2017, at 5:30 PM, Antoine Philippot <antoine.philip...@teads.tv> 
> wrote:
> 
> Thanks Piotr for your answer, we sadly can't use kafka 0.11 for now (and 
> until a while).
> 
> We can not afford tens of thousands of duplicated messages for each 
> application upgrade, can I help by working on this feature ?
> Do you have any hint or details on this part of that "todo list" ? 
>  
> 
> Le lun. 2 oct. 2017 à 16:50, Piotr Nowojski <pi...@data-artisans.com 
> <mailto:pi...@data-artisans.com>> a écrit :
> Hi,
> 
> For failures recovery with Kafka 0.9 it is not possible to avoid duplicated 
> messages. Using Flink 1.4 (unreleased yet) combined with Kafka 0.11 it will 
> be possible to achieve exactly-once end to end semantic when writing to 
> Kafka. However this still a work in progress:
> 
> https://issues.apache.org/jira/browse/FLINK-6988 
> <https://issues.apache.org/jira/browse/FLINK-6988>
> 
> However this is a superset of functionality that you are asking for. 
> Exactly-once just for clean shutdowns is also on our “TODO” list (it 
> would/could support Kafka 0.9), but it is not currently being actively 
> developed.
> 
> Piotr Nowojski
> 
>> On Oct 2, 2017, at 3:35 PM, Antoine Philippot <antoine.philip...@teads.tv 
>> <mailto:antoine.philip...@teads.tv>> wrote:
>> 
>> Hi,
>> 
>> I'm working on a flink streaming app with a kafka09 to kafka09 use case 
>> which handles around 100k messages per seconds.
>> 
>> To upgrade our application we used to run a flink cancel with savepoint 
>> command followed by a flink run with the previous saved savepoint and the 
>> new application fat jar as parameter. We notice that we can have more than 
>> 50k of duplicated messages in the kafka sink wich is not idempotent.
>> 
>> This behaviour is actually problematic for this project and I try to find a 
>> solution / workaround to avoid these duplicated messages.
>> 
>> The JobManager indicates clearly that the cancel call is triggered once the 
>> savepoint is finished, but during the savepoint execution, kafka source 
>> continue to poll new messages which will not be part of the savepoint and 
>> will be replayed on the next application start.
>> 
>> I try to find a solution with the stop command line argument but the kafka 
>> source doesn't implement StoppableFunction 
>> (https://issues.apache.org/jira/browse/FLINK-3404 
>> <https://issues.apache.org/jira/browse/FLINK-3404>) and the savepoint 
>> generation is not available with stop in contrary to cancel.
>> 
>> Is there an other solution to not process duplicated messages for each 
>> application upgrade or rescaling ?
>> 
>> If no, has someone planned to implement it? Otherwise, I can propose a pull 
>> request after some architecture advices.
>> 
>> The final goal is to stop polling source and trigger a savepoint once 
>> polling stopped.
>> 
>> Thanks
> 

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