Hi Richard,
I'm still not 100% sure, but my first guess is that it might be
because of datastore tablets splitting/merging behavior. When you
create or delete lots of entities, the datastore tablets might be
splited/merged into larger/fewer number of tablets. If that happens,
you may experience such high latencies.
This blog post by Ikai explains this issue very well:
http://ikaisays.com/2011/01/25/app-engine-datastore-tip-monotonically-increasing-values-are-bad/
Questions are:
How often those entities are created? How much QPS?
What kind of keys do you use for those small entities?
If you write entities at a somewhat high rate like >100QPS, and you're
using keys which are not distributed well, the culprit might be
splitting/merging behavior mentioned above.
Also, maybe you can consider using pull queues for such tasks.
-- Takashi
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Takashi Matsuo