Re: Corruption with duplicate primary key

On Thu, Dec 05, 2019 at 09:14:12PM +0000, Alex Adriaanse wrote:
>We have a Postgres 10 database that we recently upgraded to Postgres 12 using pg_upgrade. We recently discovered that
thereare rows in one of the tables that have duplicate primary keys:
 
>
>record_loader=# \d loader.sync
>                              Table "loader.sync"
>      Column       |           Type           | Collation | Nullable | Default
>-------------------+--------------------------+-----------+----------+---------
> source            | text                     |           | not null |
> natural_key       | text                     |           | not null |
> payload           | jsonb                    |           |          |
> dispatched        | timestamp with time zone |           | not null | now()
> initial_load_id   | text                     |           |          |
> deleted_load_id   | text                     |           |          |
> created_timestamp | timestamp with time zone |           |          | now()
> updated_timestamp | timestamp with time zone |           |          | now()
> deleted_timestamp | timestamp with time zone |           |          |
>Indexes:
>    "sync_pkey" PRIMARY KEY, btree (source, natural_key)
>Publications:
>    "debezium"
>
>This table is modified via triggers that fire off when a COPY command inserts many rows into another table.
>
>Here are two example duplicate rows:
>
># SELECT xmin, xmax, cmin, cmax, source, md5(natural_key) AS natural_key_hash, dispatched, created_timestamp,
updated_timestamp,deleted_timestamp FROM loader.sync WHERE (source, natural_key) = ('ok_lease', '...') ORDER BY
xmin::text::int,cmin::text::int;
 
>-[ RECORD 1 ]-----+---------------------------------
>xmin              | 116649
>xmax              | 0
>cmin              | 5304404
>cmax              | 5304404
>source            | ok_lease
>natural_key_hash  | de3e9a567b90025c3399c4c63c823fe9
>dispatched        | 2019-11-24 05:09:36.099686+00
>created_timestamp | 2019-11-24 05:09:36.099686+00
>updated_timestamp | 2019-11-24 05:09:36.099686+00
>deleted_timestamp |
>-[ RECORD 2 ]-----+---------------------------------
>xmin              | 116649
>xmax              | 118583
>cmin              | 5312208
>cmax              | 5312208
>source            | ok_lease
>natural_key_hash  | de3e9a567b90025c3399c4c63c823fe9
>dispatched        | 2019-11-10 05:09:24.214964+00
>created_timestamp | 2019-05-17 21:24:19.558219+00
>updated_timestamp | 2019-11-24 05:09:36.099686+00
>deleted_timestamp | 2019-11-24 05:09:36.099686+00
>
>It appears that the second row was in place originally, then got updated by a trigger (and even deleted later on,
althoughit doesn't appear that the delete transaction got committed), and then the first row was inserted within the
sametransaction that updated the second row.
 
>
>Another example:
>-[ RECORD 1 ]-----+---------------------------------
>xmin              | 116649
>xmax              | 0
>cmin              | 5304403
>cmax              | 5304403
>source            | ok_lease
>natural_key_hash  | 1c8031348701a32cb5fee26839d6b0b4
>dispatched        | 2019-11-10 05:09:24.214964+00
>created_timestamp | 2019-05-31 06:00:33.765547+00
>updated_timestamp | 2019-11-24 05:09:36.099686+00
>deleted_timestamp | 2019-11-24 05:09:36.099686+00
>-[ RECORD 2 ]-----+---------------------------------
>xmin              | 116649
>xmax              | 0
>cmin              | 5304404
>cmax              | 5304404
>source            | ok_lease
>natural_key_hash  | 1c8031348701a32cb5fee26839d6b0b4
>dispatched        | 2019-11-24 05:09:36.099686+00
>created_timestamp | 2019-11-24 05:09:36.099686+00
>updated_timestamp | 2019-11-24 05:09:36.099686+00
>deleted_timestamp |
>
>Both examples have in common that the two duplicate rows were touched within the same transaction.
>
>This database runs inside Docker, with the data directory bind-mounted to a reflink-enabled XFS filesystem. The VM is
runningDebian's 4.19.16-1~bpo9+1 kernel inside an AWS EC2 instance. We have Debezium stream data from this database via
pgoutput.
>
>Recreating the primary key confirms that the constraint doesn't (or at least shouldn't) permit these duplicate rows:
>
>record_loader=# BEGIN;
>BEGIN
>record_loader=# ALTER TABLE loader.sync DROP CONSTRAINT sync_pkey;
>ALTER TABLE
>record_loader=# ALTER TABLE loader.sync ADD CONSTRAINT sync_pkey PRIMARY KEY (source, natural_key);
>ERROR:  could not create unique index "sync_pkey"
>DETAIL:  Key (source, natural_key)=(ok_lease, ...) is duplicated.
>CONTEXT:  parallel worker
>
>Any ideas on what might cause this behavior?
>

Not sure. At first I thought maybe this might be due to collations
changing and breaking the index silently. What collation are you using?

A couple questions:

1) When you do the queries, do they use index scan or sequential scan?
Perhaps it does sequential scan, and if you force index scan (e.g. by
rewriting the query) it'll only find one of those rows.

2) Can you check in backups if this data corruption was present in the
PG10 cluster, before running pg_upgrade? 

regards

-- 
Tomas Vondra                  http://www.2ndQuadrant.com
PostgreSQL Development, 24x7 Support, Remote DBA, Training & Services