Message-ID: <546A3FBA.9020901@gmail.com>
Date: Mon, 17 Nov 2014 18:34:34 +0000
From: Tim Dudgeon <tdudgeon.ml@gmail.com>
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To: pgsql-sql@postgresql.org
Subject: slow sub-query problem
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I'm having problems optimising a query that's very slow due to a sub-query.
The query is this:

SELECT
   structure_id, batch_id, property_id, property_data
FROM chemcentral.structure_props
WHERE structure_id IN (SELECT structure_id FROM 
chemcentral.structure_props WHERE property_id = 643413)
AND property_id IN (1, 643413, 1106201);

and it takes 18s to execute.
It I replace the sub-query with the inlined 369 values so that the 4th 
line looks like this:

WHERE structure_id IN (1122687,309004,306064 ...)

it takes a few ms.

The plans are:
1. sub-query

"Nested Loop  (cost=1132.97..1182.28 rows=43 width=644) (actual 
time=70.926..18937.669 rows=381 loops=1)"
"  ->  HashAggregate  (cost=1091.73..1091.75 rows=2 width=4) (actual 
time=2.829..3.212 rows=366 loops=1)"
"        Group Key: structure_props_1.structure_id"
"        ->  Index Scan using idx_sp_property_id on structure_props 
structure_props_1  (cost=0.43..1090.77 rows=382 width=4) (actual 
time=0.033..2.380 rows=369 loops=1)"
"              Index Cond: (property_id = 643413)"
"  ->  Bitmap Heap Scan on structure_props  (cost=41.24..45.26 rows=1 
width=644) (actual time=51.726..51.727 rows=1 loops=366)"
"        Recheck Cond: ((structure_id = structure_props_1.structure_id) 
AND (property_id = ANY ('{1,643413,1106201}'::integer[])))"
"        Heap Blocks: exact=381"
"        ->  BitmapAnd  (cost=41.24..41.24 rows=1 width=0) (actual 
time=51.714..51.714 rows=0 loops=366)"
"              ->  Bitmap Index Scan on idx_sp_structure_id 
  (cost=0.00..6.80 rows=317 width=0) (actual time=0.046..0.046 rows=475 
loops=366)"
"                    Index Cond: (structure_id = 
structure_props_1.structure_id)"
"              ->  Bitmap Index Scan on idx_sp_property_id 
  (cost=0.00..33.90 rows=1146 width=0) (actual time=51.656..51.656 
rows=811892 loops=366)"
"                    Index Cond: (property_id = ANY 
('{1,643413,1106201}'::integer[]))"
"Planning time: 0.497 ms"
"Execution time: 18937.868 ms"


2. inlined values

"Bitmap Heap Scan on structure_props  (cost=2600.48..2645.29 rows=10 
width=644) (actual time=71.676..72.724 rows=381 loops=1)"
"  Recheck Cond: ((property_id = ANY ('{1,643413,1106201}'::integer[])) 
AND (structure_id = ANY 
('{1122687,309004,306064,278852,234066,1122645,412925,280033,423990,568929,448302,278487,278955,40430,40430,467979,467508,288413,289746,306073,355352,265583,4779 
(...)"
"  Heap Blocks: exact=381"
"  ->  BitmapAnd  (cost=2600.48..2600.48 rows=10 width=0) (actual 
time=71.608..71.608 rows=0 loops=1)"
"        ->  Bitmap Index Scan on idx_sp_property_id  (cost=0.00..33.90 
rows=1146 width=0) (actual time=54.614..54.614 rows=811892 loops=1)"
"              Index Cond: (property_id = ANY 
('{1,643413,1106201}'::integer[]))"
"        ->  Bitmap Index Scan on idx_sp_structure_id 
  (cost=0.00..2566.32 rows=117367 width=0) (actual time=14.487..14.487 
rows=173867 loops=1)"
"              Index Cond: (structure_id = ANY 
('{1122687,309004,306064,278852,234066,1122645,412925,280033,423990,568929,448302,278487,278955,40430,40430,467979,467508,288413,289746,306073,355352,265583,477941,326652,326602,233964,15338,397586,1122647,3088 
(...)"
"Planning time: 1.052 ms"
"Execution time: 72.858 ms"

Table is like this:

CREATE TABLE chemcentral.structure_props
(
   id serial NOT NULL,
   source_id integer NOT NULL,
   structure_id integer NOT NULL,
   batch_id character varying(16),
   parent_id integer,
   property_id integer NOT NULL,
   property_data jsonb,
   CONSTRAINT structure_props_pkey PRIMARY KEY (id)
)


All relevant columns are indexed and using PostgreSQL 9.4.
Any clues how to re-write it to avoid the slow sub-query.

Many thanks
Tim


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