LTS backport: No messages delivered after a while with PubsubIO

I am running the following Beam pipeline code locally, with the FlinkRunner. PubsubIO is used to read messages from a topic. I have a separate thread that publishes messages to the topic at regular intervals (every 30 seconds) and also sets the "ts" attribute which is used later to derive the event time.

Custom transform to convert to KV pair -

private static class PubSubMessageGrouper extends DoFn<PubsubMessage, KV<String, PubsubMessage>> {

    @ProcessElement
    public void processElement(ProcessContext c) {
        PubsubMessage element = c.element();
        KV<String, PubsubMessage> kv = KV.of(element.getAttribute("key"), element);
        c.output(kv);
    }
}

Note that "key" is a key set in the message attributes earlier in the publisher thread. The intent is to group the messages downstream by this key.

Pipeline code -

PCollection<PubsubMessage> pubsubColl = p
        .apply(PubsubIO.readMessagesWithAttributes()
            .withTimestampAttribute("ts")
            .fromTopic("projects/" + projectName + "/topics/beamtest")
        );


PCollection<KV<String, PubsubMessage>> idfied =
        pubsubColl.apply(ParDo.of(new PubSubMessageGrouper()));

PCollection<KV<String, PubsubMessage>> windowed = idfied
        .apply(Window.<KV<String, PubsubMessage>>into(FixedWindows.of(Duration.standardSeconds(15)))
            .triggering(
                Repeatedly.forever(
                    AfterWatermark.pastEndOfWindow()
                )
            )
            .withAllowedLateness(Duration.standardSeconds(15))
            .discardingFiredPanes());

PCollection<KV<String, Iterable<PubsubMessage>>> grouped = windowed.apply(GroupByKey.create());

grouped.apply(ParDo.of(new KVPrinter()));

The transforms are not chained for ease of reading. The KVPrinter transform in the end is just to print out the messages received from the group by, which will be subsequently replaced by actual code once I get this running. When I run this, I don't find the trigger executing for quite some time (a couple of minutes or longer). When it finally triggers, I see that some of the messages are not received (in the final step), not matter how long I keep it running. The Pubsub statistics in my GCP/Stackdriver dashboard show that there is a backlog of undelivered messages.

Is this due to the internal watermark that PubsubIO uses? My intention here is to make sure that all messages are processed in the groupby, including late ones within the allowed lateness window.

Note that if I remove the GroupByKey, and just print the messages after the windowing, I can see all the messages.

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An update:  I switched the .fromTopic to a .fromSubscription, with a pre-created subscription, and things have started working, as in, I can see messages being delivered now. The only difference I can see is that the automatically created subscription from within PubsubIO has an ack deadline of 60 seconds, whereas I created mine with 600 seconds (the max allowed by pubsub).

However, there is another issue now - messages don't seem to be getting acked. I keep getting redeliveries of old messages, and the Stackdriver metrics show that the num_undelivered_messages (unacked messages count) keeps on increasing. The documentation says that messages will be acked as soon as a GroupByKey or another ParDo happens, and that's happening since I am seeing the windowed groupby-s, but acks don't seem to be happening.