As I understand it vacuum operates outside of the regular transaction
and if you stop it (SIGTERM, or pg_cancel_backend()) some of the work it
accomplished will be kept when it rolls back.
For large structures with a ton of dead entries (which I seem to have a
case), running vacuum takes long enough that high-churn structures begin
to experience difficulties.
Is it reasonable to cancel and restart the vacuum process periodically
(say every 12 hours) until it manages to complete the work? It takes
about 2 hours to do the table scan, and should get in about 10 hours of
index work each round.
The vacuum ignores vacuum transaction concept looks handy right now.
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