DELETE records which do not have a match in another table

sql postgresql exists bigdata sql-delete
miloxe picture miloxe · Apr 11, 2013 · Viewed 45.7k times · Source

There are two tables linked by an id:

item_tbl (id)
link_tbl (item_id)

There are some records in item_tbl that don't have matching rows in link_tbl. A select which would count their amount would be:

SELECT COUNT(*)
FROM link_tbl lnk LEFT JOIN item_tbl itm ON lnk.item_id=itm.id
WHERE itm.id IS NULL

I would like to delete those orphan records (those which don't have match in the other table) from link_tbl but the only way I could think of was:

DELETE FROM link_tbl lnk
WHERE lnk.item_id NOT IN (SELECT itm.id FROM item_tbl itm)

There are
262,086,253 records in link_tbl
3,033,811 in item_tbl
16,844,347 orphan records in link_tbl.
The server has 4GB RAM and 8 core CPU.

EXPLAIN DELETE FROM link_tbl lnk
WHERE lnk.item_id NOT IN (SELECT itm.id FROM item_tbl itm)

Returns:

Delete on link lnk  (cost=0.00..11395249378057.98 rows=131045918 width=6)
->  Seq Scan on link lnk  (cost=0.00..11395249378057.98 rows=131045918 width=6)
     Filter: (NOT (SubPlan 1))
     SubPlan 1
       ->  Materialize  (cost=0.00..79298.10 rows=3063207 width=4)
             ->  Seq Scan on item itm  (cost=0.00..52016.07 rows=3063207 width=4)

The questions are:

  1. Is there any better way how to delete orphan records from link_tbl?

  2. How accurate is the explain above, or how long it could take to delete those records?

    • Edit: fixed according to Erwin Brandstetter comment.
    • Edit: PostgreSql version is 9.1
    • Edit: some parts of postgresql.config
      1. shared_buffers = 368MB
      2. temp_buffers = 32MB
      3. work_mem = 32MB
      4. maintenance_work_mem = 64MB
      5. max_stack_depth = 6MB
      6. fsync = off
      7. synchronous_commit = off
      8. full_page_writes = off
      9. wal_buffers = 16MB
      10. wal_writer_delay = 5000ms
      11. commit_delay = 10
      12. commit_siblings = 10
      13. effective_cache_size = 1600MB

Resolution:

Thank you all for your advices, it was very helpful. I finally used the delete advised by Erwin Brandstetter https://stackoverflow.com/a/15959896/1331340 but I tweaked it a little:

DELETE FROM link_tbl lnk
WHERE lnk.item_id BETWEEN 0 AND 10000
  AND lnk.item_id NOT IN (SELECT itm.id FROM item itm
                          WHERE itm.id BETWEEN 0 AND 10000)

I compared results for NOT IN and NOT EXISTS and the output is below, although I used COUNT instead of DELETE which I think should be the same (I mean in sake of relative comparison):

EXPLAIN ANALYZE SELECT COUNT(*) 
FROM link_tbl lnk
WHERE lnk.item_id BETWEEN 0 AND 20000
  AND lnk.item_id NOT IN (SELECT itm.id
                          FROM item_tbl itm
                          WHERE itm.id BETWEEN 0 AND 20000);

QUERY PLAN
Aggregate  (cost=6002667.56..6002667.57 rows=1 width=0) (actual time=226817.086..226817.088 rows=1 loops=1)
->  Seq Scan on link_tbl lnk  (cost=1592.50..5747898.65 rows=101907564 width=0) (actual time=206.029..225289.570 rows=566625 loops=1)
     Filter: ((item_id >= 0) AND (item_id <= 20000) AND (NOT (hashed SubPlan 1)))
     SubPlan 1
       ->  Index Scan using item_tbl_pkey on item_tbl itm  (cost=0.00..1501.95 rows=36221 width=4) (actual time=0.056..99.266 rows=17560 loops=1)
             Index Cond: ((id >= 0) AND (id <= 20000))
Total runtime: 226817.211 ms


EXPLAIN ANALYZE SELECT COUNT(*)
FROM link_tbl lnk WHERE lnk.item_id>0 AND lnk.item_id<20000
  AND NOT EXISTS (SELECT 1 FROM item_tbl itm WHERE itm.id=lnk.item_id);

QUERY PLAN
Aggregate  (cost=8835772.00..8835772.01 rows=1 width=0)
   (actual time=1209235.133..1209235.135 rows=1 loops=1)
->  Hash Anti Join  (cost=102272.16..8835771.99 rows=1 width=0)
   (actual time=19315.170..1207900.612 rows=566534 loops=1)
     Hash Cond: (lnk.item_id = itm.id)
     ->  Seq Scan on link_tbl lnk  (cost=0.00..5091076.55 rows=203815128 width=4) (actual time=0.016..599147.604 rows=200301872 loops=1)
           Filter: ((item_id > 0) AND (item_id < 20000))
     ->  Hash  (cost=52016.07..52016.07 rows=3063207 width=4) (actual time=19313.976..19313.976 rows=3033811 loops=1)
           Buckets: 131072  Batches: 4  Memory Usage: 26672kB
           ->  Seq Scan on item_tbl itm  (cost=0.00..52016.07 rows=3063207 width=4) (actual time=0.013..9274.158 rows=3033811 loops=1)
Total runtime: 1209260.228 ms

NOT EXISTS was 5 times slower.

The actual delete of the data didn't take so long as I was worried, I was able to delete it in 5 batches (10000-20000,20000-100000,100000-200000,200000-1000000 and 1000000-1755441). At first I found out max item_id and I only had to went through half of the table.

When I tried NOT IN or EXISTS without the range (with select count) it didn't even finish, I let it run during the night and it was still running in the morning.

I think I was looking for DELETE with USING from wildplasser's answer https://stackoverflow.com/a/15988033/1331340 but it came too late.

DELETE FROM one o
USING (
    SELECT o2.id
    FROM one o2
    LEFT JOIN two t ON t.one_id = o2.id
    WHERE t.one_id IS NULL
    ) sq
WHERE sq.id = o.id
    ;

Answer

wildplasser picture wildplasser · Apr 13, 2013

I benchmarked four typical queries, with different settings for {work_mem, effective_cache_size, random_page_cost}, these settings have the largest influence on the selected plan. I first did a "run in" with my default settings to warm the cache. Note: the test-set is small enough to allow all needed pages to be present in cache.

The test-set

SET search_path=tmp;

/************************/
DROP SCHEMA tmp CASCADE;
CREATE SCHEMA tmp ;
SET search_path=tmp;

CREATE TABLE one
        ( id SERIAL NOT NULL PRIMARY KEY
        , payload varchar
        );

CREATE TABLE two
        ( id SERIAL NOT NULL PRIMARY KEY
        , one_id INTEGER REFERENCES one
        , payload varchar
        );

INSERT INTO one (payload) SELECT 'Text_' || gs::text FROM generate_series(1,30000) gs;
INSERT INTO two (payload) SELECT 'Text_' || gs::text FROM generate_series(1,30000) gs;


UPDATE two t
SET one_id = o.id
FROM one o
WHERE o.id = t.id
AND random() < 0.1;

INSERT INTO two (one_id,payload) SELECT one_id,payload FROM two;
INSERT INTO two (one_id,payload) SELECT one_id,payload FROM two;
INSERT INTO two (one_id,payload) SELECT one_id,payload FROM two;

VACUUM ANALYZE one;
VACUUM ANALYZE two;
/***************/

The queries:

\echo NOT EXISTS()
EXPLAIN ANALYZE
DELETE FROM one o
WHERE NOT EXISTS ( SELECT * FROM two t
        WHERE t.one_id = o.id
        );

\echo NOT IN()
EXPLAIN ANALYZE 
DELETE FROM one o
WHERE o.id NOT IN ( SELECT one_id FROM two t)
        ;

\echo USING (subquery self LEFT JOIN two where NULL)
EXPLAIN ANALYZE
DELETE FROM one o
USING (
        SELECT o2.id
        FROM one o2
        LEFT JOIN two t ON t.one_id = o2.id
        WHERE t.one_id IS NULL
        ) sq
WHERE sq.id = o.id
        ;

\echo USING (subquery self WHERE NOT EXISTS(two)))
EXPLAIN ANALYZE
DELETE FROM one o
USING (
        SELECT o2.id
        FROM one o2
        WHERE NOT EXISTS ( SELECT *
                FROM two t WHERE t.one_id = o2.id
                )
        ) sq
WHERE sq.id = o.id
        ;

The result (summarised)

                        NOT EXISTS()    NOT IN()        USING(LEFT JOIN NULL)   USING(NOT EXISTS)
1) rpc=4.0.csz=1M wmm=64        80.358  14389.026       77.620                  72.917
2) rpc=4.0.csz=1M wmm=64000     60.527  69.104          51.851                  51.004
3) rpc=1.5.csz=1M wmm=64        69.804  10758.480       80.402                  77.356
4) rpc=1.5.csz=1M wmm=64000     50.872  69.366          50.763                  53.339
5) rpc=4.0.csz=1G wmm=64        84.117  7625.792        69.790                  69.627
6) rpc=4.0.csz=1G wmm=64000     49.964  67.018          49.968                  49.380
7) rpc=1.5.csz=1G wmm=64        68.567  3650.008        70.283                  69.933
8) rpc=1.5.csz=1G wmm=64000     49.800  67.298          50.116                  50.345

legend: 
rpc := "random_page_cost"
csz := "effective_cache_size"
wmm := "work_mem"

As you can see, the NOT IN() variant is very sensitive to shortage of work_mem. Agreed, the setting 64(KB) is very low, but this `more or less* corresponds to large data sets, which won't fit in hashtables, either.

EXTRA: during the warm-in phase, the NOT EXISTS() query suffered from extreme FK-trigger contention. This apears to be a result of a conflict with the vacuum deamon, which is still active after the table set-up.:

PostgreSQL 9.1.2 on x86_64-unknown-linux-gnu, compiled by gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1, 64-bit
NOT EXISTS()
                                                           QUERY PLAN
--------------------------------------------------------------------------------------------------------------------------------
 Delete on one o  (cost=6736.00..7623.94 rows=27962 width=12) (actual time=80.596..80.596 rows=0 loops=1)
   ->  Hash Anti Join  (cost=6736.00..7623.94 rows=27962 width=12) (actual time=49.174..61.327 rows=27050 loops=1)
         Hash Cond: (o.id = t.one_id)
         ->  Seq Scan on one o  (cost=0.00..463.00 rows=30000 width=10) (actual time=0.003..5.156 rows=30000 loops=1)
         ->  Hash  (cost=3736.00..3736.00 rows=240000 width=10) (actual time=49.121..49.121 rows=23600 loops=1)
               Buckets: 32768  Batches: 1  Memory Usage: 1015kB
               ->  Seq Scan on two t  (cost=0.00..3736.00 rows=240000 width=10) (actual time=0.006..33.790 rows=240000 loops=1)
 Trigger for constraint two_one_id_fkey: time=467720.117 calls=27050
 Total runtime: 467824.652 ms
(9 rows)

Related questions

Select rows which are not present in other table

I've got two postgresql tables: table name column names ----------- ------------------------ login_log ip | etc. ip_location ip | location | hostname | etc. I want to get every IP address from login_log which doesn't have a row in ip_location. I …

Read More
PL/pgSQL checking if a row exists

I'm writing a function in PL/pgSQL, and I'm looking for the simplest way to check if a row exists. Right now I'm SELECTing an integer into a boolean, which doesn't really work. I'm not experienced with PL/pgSQL enough …

Read More
Find difference between two big tables in PostgreSQL

I have two similar tables in Postgres with just one 32-byte latin field (simple md5 hash). Both tables have ~30,000,000 rows. Tables have little difference (10-1000 rows are different) Is it possible with Postgres to find a difference between these tables, …

Read More