I have a table in my database which is occupying 161GB hard disk space. Only 5 gb free space is left out of 200Gb harddisk.
The following command shows that my table is consuming 161GB harddisk space,
select pg_size_pretty(pg_total_relation_size('Employee'));
There are close to 527 rows in the table. Now I deleted 250 rows. Again I checked the pg_total_relation_size of Employee. Still the size is 161GB.
After seeing the output of the above query, I ran the vacuum command:
VACUUM VERBOSE ANALYZE Employee;
I checked if the VACUUM actually happened using,
SELECT relname, last_vacuum, last_autovacuum FROM pg_stat_user_tables;
I can see the last vacuum time matching the time I ran the VACUUM command.
I also ran the below command to see if there any dead tuples,
SELECT relname, n_dead_tup FROM pg_stat_user_tables;
n_dead_tup count for Employee table is 0.
Still after all these above commands if I run,
select pg_size_pretty(pg_total_relation_size('Employee'));
it still shows 161GB.
May I please know the reason behind this? Also please correct me on how to free interface_list.
vacuum doesn't physically "free" space. It only marks no longer used space as re-usable. So subsequent UPDATE or INSERT statements can use that space instead of appending to the table.
Quote from the manual
The standard form of VACUUM removes dead row versions in tables and indexes and marks the space available for future reuse. However, it will not return the space to the operating system, except in the special case where one or more pages at the end of a table become entirely free and an exclusive table lock can be easily obtained
(emphasis mine)
If you re-insert the 250 deleted rows, you will see that the table doesn't grow again, as the newly inserted rows simply use the space that was marked free by vacuum.
If you actually want to physically reduce the size of the table to size that is "needed", you need to run vacuum full.
Quote from the manual
VACUUM FULL actively compacts tables by writing a complete new version of the table file with no dead space. This minimizes the size of the table, but can take a long time. It also requires extra disk space for the new copy of the table, until the operation completes
(emphasis mine)
Related
We've noticed one of our tables growing considerably on PG 12. This table is the target of very frequent updates, with a mix of column types, including a very large text column (often with over 50kb of data) - we run a local cron job that looks for rows older than X time and set the text column to a null value (as we no longer need the data for that particular column after X amount of time).
We understand this does not actually free up disk space due to the MVCC model, but we were hoping that auto-vacuum would take care of this. To our surprise, the table continues to grow (now over 40gb worth) without auto-vacuum running. Running a vacuum manually has addressed the issue and we no longer see growth.
This has lead me to investigate other tables, I'm realising that I don't understand how auto-vacuum is triggered at all.
Here is my understanding of how it works, which hopefully someone can pick apart:
I look for tables that have a large amount of dead tuples in them:
select * from pg_stat_all_tables ORDER BY n_dead_tup desc;
I identify tableX with 33169557 dead tuples (n_dead_tup column).
I run a select * from pg_class ORDER BY reltuples desc; to check how many estimated rows there are on table tableX
I identify 1725253 rows via the reltuples column.
I confirm my autovacuum settings: autovacuum_vacuum_threshold = 50 and autovacuum_vacuum_scale_factor = 0.2
I apply the formula threshold + pg_class.reltuples * scale_factor, so, 50 + 1725253 * 0.2 which returns 345100.6
It is my understanding that auto-vacuum will start on this table once ~345100 dead tuples are found. But tableX is already at a whopping 33169557 dead tuples!, The last_autovacuum on this table was back in February.
Any clarification would be welcome.
Your algorithm is absolutely correct.
Here are some reasons why things could go wrong:
autovacuum runs, but is so slow that it never gets done
If you see no running autovacuum, that is not your problem.
autovacuum runs, but a long running open transaction prevents it from removing dead tuples
other tables need to be vacuumed more urgently (to avoid transaction ID wraparound), so the three workers are busy with other things
autovacuum runs, but conflicts with high concurrent locks on the table (LOCK TABLE, ALTER TABLE, ...)
This makes autovacuum give up and try again later.
autovacuum is disabled, perhaps only for that table
I have a bloated table, its name is "role_info".
There are about 20K insert operations and a lot of update operations per day, there are no delete operations.
The table is about 4063GB now.
We have migrated the table to another database using dump, and the new table is about 62GB, so the table on the old database is bloated very seriously.
PostgreSQL version: 9.5.4
The table schema is below:
CREATE TABLE "role_info" (
"roleId" bigint NOT NULL,
"playerId" bigint NOT NULL,
"serverId" int NOT NULL,
"status" int NOT NULL,
"baseData" bytea NOT NULL,
"detailData" bytea NOT NULL,
PRIMARY KEY ("roleId")
);
CREATE INDEX "idx_role_info_serverId_playerId_roleId" ON "role_info" ("serverId", "playerId", "roleId");
The average size of field 'detailData' is about 13KB each line.
There are some SQL execution results below:
1)
SELECT
relname AS name,
pg_stat_get_live_tuples(c.oid) AS lives,
pg_stat_get_dead_tuples(c.oid) AS deads
FROM pg_class c
ORDER BY deads DESC;
Execution Result:
2)
SELECT *,
Pg_size_pretty(total_bytes) AS total,
Pg_size_pretty(index_bytes) AS INDEX,
Pg_size_pretty(toast_bytes) AS toast,
Pg_size_pretty(table_bytes) AS TABLE
FROM (SELECT *,
total_bytes - index_bytes - Coalesce(toast_bytes, 0) AS
table_bytes
FROM (SELECT c.oid,
nspname AS table_schema,
relname AS TABLE_NAME,
c.reltuples AS row_estimate,
Pg_total_relation_size(c.oid) AS total_bytes,
Pg_indexes_size(c.oid) AS index_bytes,
Pg_total_relation_size(reltoastrelid) AS toast_bytes
FROM pg_class c
LEFT JOIN pg_namespace n
ON n.oid = c.relnamespace
WHERE relkind = 'r') a
WHERE table_schema = 'public'
ORDER BY total_bytes DESC) a;
Execution Result:
3)
I have tried to vacuum full the table "role_info", but it seemed blocked by some other process, and didn't execute at all.
select * from pg_stat_activity where query like '%VACUUM%' and query not like '%pg_stat_activity%';
Execution Result:
select * from pg_locks;
Execution Result:
There are parameters of vacuum:
I have two questions:
How to deal with table bloating? autovacuum seems not working.
Why did the vacuum full blocked?
With your autovacuum settings, it will sleep for 20ms once for every 10 pages (200 cost_limit / 20 cost_dirty) it dirties. Even more because there will also be cost_hit and cost_miss as well. At that rate is would take over 12 days to autovacuum a 4063GB table which is mostly in need of dirtying pages. That is just the throttling time, not counting the actual work-time, nor the repeated scanning of the indexes. So it the actual run time could be months. The chances of autovacuum getting to run to completion in one sitting without being interrupted by something could be pretty low. Does your database get restarted often? Do you build and drop indexes on this table a lot, or add and drop partitions, or run ALTER TABLE?
Note that in v12, the default setting of autovacuum_vacuum_cost_delay was lowered by a factor of 10. This is not just because of some change to the code in v12, it was because we realized the default setting was just not sensible on modern hardware. So it would probably make sense to backport this change your existing database, if not go even further. Before 12, you can't lower to less than 1 ms, but you could lower it to 1 ms and also either increase autovacuum_vacuum_cost_delay or lower vacuum_cost_page_* setting.
Now this analysis is based on the table already being extremely bloated. Why didn't autovacuum prevent it from getting this bloated in the first place, back when the table was small enough to be autovacuumed in a reasonable time? That is hard to say. We really have no evidence as to what happened back then. Maybe your settings were even more throttled than they are now (although unlikely as it looks like you just accepted the defaults), maybe it was constantly interrupted by something. What is the "autovacuum_count" from pg_stat_all_tables for the table and its toast table?
Why did the vacuum full blocked?
Because that is how it works, as documented. That is why it is important to avoid getting into this situation in the first place. VACUUM FULL needs to swap around filenodes at the end, and needs an AccessExclusive lock to do that. It could take a weaker lock at first and then try to upgrade to AccessExclusive later, but lock upgrades have a strong deadlock risk, so it takes the strongest lock it needs up front.
You need a maintenance window where no one else is using the table. If you think you are already in such window, then you should look at the query text for the process doing the blocking. Because the lock already held is ShareUpdateExclusive, the thing holding it is not a normal query/DML, but some kind of DDL or maintenance operation.
If you can't take a maintenance window now, then you can at least do a manual VACUUM without the FULL. This takes a much weaker lock. It probably won't shrink the table dramatically, but should at least free up space for internal reuse so it stops getting even bigger while you figure out when you can schedule a maintenance window or what your other next steps are.
I have a very simple query that is taking way too long to run.
SELECT DISTINCT col1,col2,col3,col4 FROM tbl1;
What indexes do I need to add to speed up? I ran a simple vacuum; command and added the following index but neither helped.
CREATE INDEX tbl_idx ON tbl1(col1,col2,col3,col4);
The table has 400k rows. In fact counting them is taking extremely long as well. Running a simple
SELECT count(*) from tbl1;
is taking 8 seconds. So it's possible my problems are with vacuuming or reindexing or something I'm not sure.
Here is the explain command
EXPLAIN SELECT DISTINCT col1,col2,col3,col4 FROM tbl1;
QUERY PLAN
---------------------------------------------------------------------------------
Unique (cost=3259846.80..3449267.51 rows=137830 width=25)
-> Sort (cost=3259846.80..3297730.94 rows=15153657 width=25)
Sort Key: col1, col2, col3, col4
-> Seq Scan on tbl1 (cost=0.00..727403.57 rows=15153657 width=25)
(4 rows)
Edit: I'm currently running vacuum full; which hopefully fixes the issue and then maybe someone can give me some pointers on how to fix where I went wrong. It is several hours in and still going as far as I can tell. I did run
select relname, last_autoanalyze, last_autovacuum, last_vacuum, n_dead_tup from pg_stat_all_tables where n_dead_tup >0;
and the table has nearly 16 million n_dead_tup rows.
My data doesn't change that frequently so I ended up creating a materialized view
CREATE MATERIALIZED VIEW tbl1_distinct_view AS SELECT DISTINCT col1,col2,col3,col4 FROM tbl1;
that I refresh with a cronjob once a day at 6am
0 6 * * * psql -U mydb mydb -c 'REFRESH MATERIALIZED VIEW tbl1_distinct_view;
try force database to use your index
set enable_seqscan=off ;
SELECT DISTINCT col1,col2,col3,col4 FROM tbl1;
set enable_seqscan=on ;
VACUUM and VACUUM FULL are two commands that sound the same but have very different effects.
VACUUM scans a table for tuples that it no longer needs, so that it can overwrite that space during INSERT or UPDATE statements. This command only looks at deleted rows, and does not "defragment" the table - it leaves the space usage the same, but simply marks some space as "dead" in order that it can be reused.
VACUUM FULL looks at every row, and reclaims the space left by deleted rows and dead tuples, essentially "defragmenting" the table. If this is done on a live table, it can take a very long time, and can result in heavy weight locks, increased IO, and index bloat.
I imagine what you need is a VACUUM followed by an ANALYZE, which will rebuild your statistics for each table, improving index performance. These should be performed reasonably regularly in low-usage times for a database. Only if you have a lot of space to reclaim (due to lots of DELETE statements) should you use VACUUM FULL.
Anyhow, since you've run a VACUUM FULL, once that it complete you should run an ANALYZE on the database, followed by a REINDEX (on the database), and then an EXPLAIN on your query again, you should notice an improvement.
According to AWS doc:
Amazon Redshift does not automatically reclaim and reuse space that is freed when you delete rows and update rows.
Before running VACUUM, is there a way to know or evaluate how much space will be free from disk by the VACUUM?
Thx
References:
http://docs.aws.amazon.com/redshift/latest/dg/t_Reclaiming_storage_space202.html
http://docs.aws.amazon.com/redshift/latest/dg/r_VACUUM_command.html
You can calculate the amount of storage that will be freed up from a vacuum command by looking up the tbl_rows column in the svv_table_info view. This includes rows that are marked for deletion. Compare that to a select count(*) from the same table and you'll have a ratio. Something like this on a theoretical table named factsales.
select (select cast(count(*) as numeric(12,0)) from factsales) /
cast(tbl_rows as numeric(12,0))
as "percentage of non deleted rows"
from svv_table_info where "table" = 'factsales'
There doesn't appear to be a straightforward way to execute dynamic SQL and cursors so to get this same ratio across all tables you'd have to execute the code from an external source or programming language i.e. python.
Its not an extremely accurate way, but you can query svv_table_info and look for the column deleted_pct. This will give you a rough idea, in percentage terms, about what fraction of the table needs to be rebuilt using vacuum.
You can run it for all the tables in your system to get this estimate for the whole system.
I have made a backup of my PostgreSQL database using pg_dump to ".sql" file.
When I restored the database, its size was 2.8GB compared with 3.7GB of the source (original) database. The application that access the database appears to work fine.
What is the reason to smaller size of the restored database?
The short answer is that database storage is more optimised for speed than space.
For instance, if you inserted 100 rows into a table, then deleted every row with an odd numbered ID, the DBMS could write out a new table with only 50 rows, but it's more efficient for it to simply mark the deleted rows as free space and reuse them when you next insert a row. Therefore the table takes up twice as much space as is currently needed.
Postgres's use of "MVCC", rather than locking, for transaction management makes this even more likely, since an UPDATE usually involves writing a new row to storage, then marking the old row deleted once no transactions are looking at it.
By dumping and restoring the database, you are recreating a DB without all this free space. This is essentially what the VACUUM FULL command does - it rewrites the current data into a new file, then deletes the old file.
There is an extension distributed with Postgres called pg_freespace which lets you examine some of this. e.g. you can list the main table size (not including indexes and columns stored in separate "TOAST" tables) and free space used by each table with the below:
Select oid::regclass::varchar as table,
pg_size_pretty(pg_relation_size(oid)/1024 * 1024) As size,
pg_size_pretty(sum(free)) As free
From (
Select c.oid,
(pg_freespace(c.oid)).avail As free
From pg_class c
Join pg_namespace n on n.oid = c.relnamespace
Where c.relkind = 'r'
And n.nspname Not In ('information_schema', 'pg_catalog')
) tbl
Group By oid
Order By pg_relation_size(oid) Desc, sum(free) Desc;
The reason is simple: during its normal operation, when rows are updated, PostgreSQL adds a new copy of the row and marks the old copy of the row as deleted. This is multi-version concurrency control (MVCC) in action. Then VACUUM reclaims the space taken by the old row for data that can be inserted in the future, but doesn't return this space to the operating system as it's in the middle of a file. Note that VACUUM isn't executed immediately, only after enough data has been modified in the table or deleted from the table.
What you're seeing is entirely normal. It just shows that PostgreSQL database will be larger in size than the sum of the sizes of the rows. Your new database will most likely eventaully grow to 3.7GB when you start actively using it.