High number of live/dead tuples in postgresql/ Vacuum not working - postgresql

Question

There is a table , which has 200 rows . But number of live tuples showing there is more than that (around 60K) .
select count(*) from subscriber_offset_manager;
count
-------
200
(1 row)
SELECT schemaname,relname,n_live_tup,n_dead_tup FROM pg_stat_user_tables where relname='subscriber_offset_manager' ORDER BY n_dead_tup
;
schemaname | relname | n_live_tup | n_dead_tup
------------+---------------------------+------------+------------
public | subscriber_offset_manager | 61453 | 5
(1 row)
But as seen from pg_stat_activity and pg_locks , we are not able to track any open connection .
SELECT query, state,locktype,mode
FROM pg_locks
JOIN pg_stat_activity
USING (pid)
WHERE relation::regclass = 'subscriber_offset_manager'::regclass
;
query | state | locktype | mode
-------+-------+----------+------
(0 rows)
I also tried full vacuum on this table , Below are results :
All the times no rows are removed
some times all the live tuples become dead tuples .
Here is output .
vacuum FULL VERBOSE ANALYZE subscriber_offset_manager;
INFO: vacuuming "public.subscriber_offset_manager"
INFO: "subscriber_offset_manager": found 0 removable, 67920 nonremovable row versions in 714 pages
DETAIL: 67720 dead row versions cannot be removed yet.
CPU 0.01s/0.06u sec elapsed 0.13 sec.
INFO: analyzing "public.subscriber_offset_manager"
INFO: "subscriber_offset_manager": scanned 710 of 710 pages, containing 200 live rows and 67720 dead rows; 200 rows in sample, 200 estimated total rows
VACUUM
SELECT schemaname,relname,n_live_tup,n_dead_tup FROM pg_stat_user_tables where relname='subscriber_offset_manager' ORDER BY n_dead_tup
;
schemaname | relname | n_live_tup | n_dead_tup
------------+---------------------------+------------+------------
public | subscriber_offset_manager | 200 | 67749
and after 10 sec
SELECT schemaname,relname,n_live_tup,n_dead_tup FROM pg_stat_user_tables where relname='subscriber_offset_manager' ORDER BY n_dead_tup
;
schemaname | relname | n_live_tup | n_dead_tup
------------+---------------------------+------------+------------
public | subscriber_offset_manager | 68325 | 132
How Our App query to this table .
Our application generally select some rows and based on some business calculation, update the row .
select query -- select based on some id
select * from subscriber_offset_manager where shard_id=1 ;
update query -- update some other column for this selected shard id
around 20 threads do this in parallel and One thread works on only one row .
app is writen in java and we are using hibernate to do db operations .
Postgresql version is 9.3.24
One more interesting observation :
- when i stop my java app and then do full vacuum , it works fine (number of rows and live tuples become equal). So there is something wrong if we select and update continuously from java app . –
Problem/Issue
These live tuples some times go to dead tuples and after some times again comes to live .
Due to above behaviour select from the table taking time and increasing load on server as lots of live/deadtuples are there ..

Answer 1

I know three things that keep VACUUM from doing its job:
Long running transactions.
Prepared transactions that did not get committed.
Stale replication slots.
See my blog post for details.

Answer 2

I got the issue ☺ .
For Understanding the issue consider the following flow :
Thread 1 -
Opens a hibernate session
Make some queries on Table-A
Select from subscriber_offset_manager
Update subscriber_offset_manager .
Closes the Session .
Many Threads of Type Thread-1 running in parallel .
Thread 2 -
These type of threads are running in parallel .
Opens a hibernate session
Make some select queries on Table-A
Does not close session .(session leak .)
Temporary Solution - If i close all those connection made by Thread-2 by using pg_cancel_backend then vacuuming starts working .
Also we have recreated the issue many times and tried this solution and it worked .
Now, there are following doubts which are still not answered .
Why postgres is not showing any data related to table "subscriber_offset_manager" .
This issue is not re-creating when instead of running Thread-2 , if we run select on Table-A , using psql .
why postgres is working like this with jdbc .
Some more mind blowing observation :
event if we run queries on "subscriber_offset_manager" in different session then also issue coming ;
we found many instance here where Thread 2 is working on some third table "Table-C" and issue is coming
all these type od transactions state in pg_stat_activity is "idle_in_transaction ."
#Erwin Brandstetter and #Laurenz Albe , if you know there is bug related to postgres/jdbc .

Answer 3

There might be locks after all, your query might be misleading:
SELECT query, state,locktype,mode
FROM pg_locks
JOIN pg_stat_activity USING (pid)
WHERE relation = 'subscriber_offset_manager'::regclass
pg_locks.pid can be NULL, then the join would eliminate rows. The manual for Postgres 9.3:
Process ID of the server process holding or awaiting this lock, or null if the lock is held by a prepared transaction
Bold emphasis mine. (Still the same in pg 10.)
Do you get anything for the simple query?
SELECT * FROM pg_locks
WHERE relation = 'subscriber_offset_manager'::regclass;
This could explain why VACUUM complains:
DETAIL: 67720 dead row versions cannot be removed yet.
This, in turn, would point to problems in your application logic / queries, locking more rows than necessary.
My first idea would be long running transactions, where even a simple SELECT (acquiring a lowly ACCESS SHARE lock) can block VACUUM from doing its job. 20 threads in parallel might chain up and lock out VACUUM indefinitely. Keep your transactions (and their locks) as brief as possible. And make sure your queries are optimized and don't lock more rows than necessary.
One more thing to note: transaction isolation levels SERIALIZABLE or REPEATABLE READ make it much harder for VACUUM to clean up. Default READ COMMITTED mode is less restrictive, but VACUUM can still be blocked as discussed.
Related:
What are the consequences of not ending a database transaction?
Postgres UPDATE … LIMIT 1
VACUUM VERBOSE outputs, nonremovable “dead row versions cannot be removed yet”?