Postgres NOT IN performance

Question

Any ideas how to speed up this query?

Input

EXPLAIN SELECT entityid FROM entity e

LEFT JOIN level1entity l1 ON l1.level1id = e.level1_level1id
LEFT JOIN level2entity l2 ON l2.level2id = l1.level2_level2id
WHERE 

l2.userid = 'a987c246-65e5-48f6-9d2d-a7bcb6284c8f' 
AND 
(entityid NOT IN 
(1377776,1377792,1377793,1377794,1377795,1377796... 50000 ids)
)

Output

Nested Loop  (cost=0.00..1452373.79 rows=3865 width=8)
  ->  Nested Loop  (cost=0.00..8.58 rows=1 width=8)
        Join Filter: (l1.level2_level2id = l2.level2id)
        ->  Seq Scan on level2entity l2  (cost=0.00..3.17 rows=1 width=8)
              Filter: ((userid)::text = 'a987c246-65e5-48f6-9d2d-a7bcb6284c8f'::text)
        ->  Seq Scan on level1entity l1  (cost=0.00..4.07 rows=107 width=16)
  ->  Index Scan using fk_fk18edb1cfb2a41235_idx on entity e  (cost=0.00..1452086.09 rows=22329 width=16)
        Index Cond: (level1_level1id = l1.level1id)

OK here a simplified version, the joins aren't the bottleneck

SELECT enitityid FROM 
(SELECT enitityid FROM enitity e LIMIT 5000) a

WHERE
(enitityid NOT IN 
(1377776,1377792,1377793,1377794,1377795, ... 50000 ids)
)

the problem is to find the enties which don't have any of these ids

EXPLAIN

Subquery Scan on a  (cost=0.00..312667.76 rows=1 width=8)
  Filter: (e.entityid <> ALL ('{1377776,1377792,1377793,1377794, ... 50000 ids}'::bigint[]))
  ->  Limit  (cost=0.00..111.51 rows=5000 width=8)
        ->  Seq Scan on entity e  (cost=0.00..29015.26 rows=1301026 width=8)

Answer 1

A huge IN list is very inefficient. PostgreSQL should ideally identify it and turn it into a relation that it does an anti-join on, but at this point the query planner doesn't know how to do that, and the planning time required to identify this case would cost every query that uses NOT IN sensibly, so it'd have to be a very low cost check. See this earlier much more detailed answer on the topic.

As David Aldridge wrote this is best solved by turning it into an anti-join. I'd write it as a join over a VALUES list simply because PostgreSQL is extremely fast at parsing VALUES lists into relations, but the effect is the same:

SELECT entityid 
FROM entity e
LEFT JOIN level1entity l1 ON l.level1id = e.level1_level1id
LEFT JOIN level2entity l2 ON l2.level2id = l1.level2_level2id
LEFT OUTER JOIN (
    VALUES
    (1377776),(1377792),(1377793),(1377794),(1377795),(1377796)
) ex(ex_entityid) ON (entityid = ex_entityid)
WHERE l2.userid = 'a987c246-65e5-48f6-9d2d-a7bcb6284c8f' 
AND ex_entityid IS NULL; 

For a sufficiently large set of values you might even be better off creating a temporary table, COPYing the values into it, creating a PRIMARY KEY on it, and joining on that.

More possibilities explored here:

https://stackoverflow.com/a/17038097/398670