[postgis-users] Performance issue with ST_INTERSECTS

[Shira Bezalel]

Hello List, 

This is my first post so feel free to let me know if I'm missing any critical info or if this is better suited for the pgsql-performance list. 

Essentially, I'm troubleshooting a performance issue with a spatial intersection query. The query sums the lengths of line features that intersect polygon features. The line layer is very dense. The polygon layer only has 8 features, but each polygon does have a lot of points.

It's taking almost 50 minutes to run and I'm wondering if the planner is choosing a less than optimal query plan. One reason I'm thinking this is based on a bad row estimate in the explain analyze output. Can anything be done to resolve this bad estimate? Or is it unavoidable? And more importantly: Is the query plan that the planner is choosing the fastest one that it could use despite the bad row estimate? 

-----Version Info----- 
Production Server: 
PostgreSQL 8.4.7 on x86_64-pc-linux-gnu, compiled by GCC gcc-4.4.real (Ubuntu 4.4.3-4ubuntu5) 4.4.3, 64-bit 
POSTGIS="1.5.1" GEOS="3.2.2-CAPI-1.6.2" PROJ="Rel. 4.7.1, 23 September 2009 " LIBXML="2.7.6" USE_STATS

We also tested the query against a test server with more recent postgres product versions (the same query plan and bad row estimate occurred): 
PostgreSQL 9.1.1 on x86_64-pc-linux-gnu, compiled by gcc-4.6.real (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1, 64-bit 
POSTGIS="1.5.3" GEOS="3.2.2-CAPI-1.6.2" PROJ="Rel. 4.7.1, 23 September 2009 " LIBXML="2.7.8" USE_STATS (procs from 1.5 r5385 need upgrade)

-----SQL Statement----- 
SELECT r.gid, SUM(ST_LENGTH(ST_INTERSECTION(r.the_geom,n.the_geom))) * 0.000621371192 AS milesum 
FROM psaregions r join nhd100kstreams n ON ST_INTERSECTS(r.the_geom, n.the_geom) 
WHERE n.fcode = 46003 
GROUP BY r.gid 

-----Explain Analyze Output----- 

See here: http://explain.depesz.com/s/Esx 

HashAggregate (cost=509.88..512.02 rows=8 width=1195362) (actual time=2823674 .455..2823674 .458 rows=8 loops=1) 
-> Nested Loop (cost=0.00..70.36 rows=87904 width=1195362) (actual time=23.893..675119.593 rows=90268 loops=1) 
Join Filter: _st_intersects(r.the_geom, n.the_geom) 
-> Seq Scan on psaregions r (cost=0.00..1.08 rows=8 width=1193798) (actual time=0.005..0.019 rows=8 loops=1) 
-> Index Scan using nhd100kstreams_the_geom_gist on nhd100kstreams n (cost=0.00..8.40 rows=1 width=1564) (actual time=0.043..214.728 rows=41631 loops=8) 
Index Cond: (r.the_geom && n.the_geom) 
Filter: (n.fcode = 46003) 
Total runtime: 2823674.517 ms 

***Notice actual rows in the first index scan is 41631, but the estimate is 1. 

-----Additional Info----- 
- I've run vacuum analyze on the tables in question. That has not helped. (Autovacuum does run regularly also.) 
- In terms of history, this query has always been slow. 
- Various configuration settings: 
shared_buffers: 3GB (Machine RAM: 12GB) 
work_mem: 2GB 
maintenance_work_mem: 1GB 
effective_cache_size: 2GB (this was originally set to the default; we increased it to 2GB and restarted the server, but it didn't change the query plan.) 
- Hardware info: Dell PowerEdge R710 running Ubuntu 10.04.2 LTS. 

-----Table and Index Schema----- 

Table "public.psaregions" 
Column | Type | Modifiers 
------------+-----------------------+---------------------------------------------------------- 
gid | integer | not null default nextval('psaregions_gid_seq'::regclass) 
psa_region | character varying(50) | 
np_length | numeric | 
xxx | numeric | 
the_geom | geometry | 
sm_geom | geometry | 
miles46006 | numeric | 
miles46003 | numeric | 
llextent | character varying | 
Indexes: 
"psaregions_pkey" PRIMARY KEY, btree (gid) 
"psaregions_region_idx" btree (psa_region) 
"psaregions_sm_geom_gist" gist (sm_geom) 
"psaregions_the_geom_gist" gist (the_geom) 


Table "public.nhd100kstreams" 
Column | Type | Modifiers 
------------+-----------------------+-------------------------------------------------------------- 
gid | integer | not null default nextval('nhd100kstreams_gid_seq'::regclass) 
objectid | integer | 
comid | integer | 
fdate | date | 
resolution | integer | 
gnis_id | character varying(10) | 
gnis_name | character varying(65) | 
lengthkm | numeric | 
reachcode | character varying(14) | 
flowdir | integer | 
wbareacomi | integer | 
ftype | integer | 
fcode | integer | 
shape_leng | numeric | 
enabled | smallint | 
geo_geom | geometry | 
sm_geom | geometry | 
the_geom | geometry | 
Indexes: 
"nhd100kstreams_pkey" PRIMARY KEY, btree (gid) 
"nhd100kstreams_fcode_idx" btree (fcode) 
"nhd100kstreams_geo_geom_gist" gist (geo_geom) 
"nhd100kstreams_sm_geom_gist" gist (sm_geom) 
"nhd100kstreams_the_geom_gist" gist (the_geom) 


-----Table Metadata: ----- 
psaregions: 8 records; very static, no regular updates/inserts 
nhd100kstreams: 234954 records; 137,676 records with fcode = 46003; very static, no regular updates/inserts


Looking forward to hearing your feedback. 

Thank you kindly, 
Shira Bezalel