PostgreSQL 9.3.10 – How to Improve Slow Performance of Maintenance/Deletion Query

postgresqlpostgresql-9.3

I have a reddit-type app called 'Links' where 1) users post interesting hyperlinks, and 2) other users publicly respond to such postings. The former is defined as links_link table in my postgresql 9.3.10 DB, the latter is links_publicreply.

I've noticed that deletion is quite fast across most of the tables in the DB of this web app.

However, links_publicreply is problematic. E.g., I just deleted 238 rows from that table, and waited for ~20 mins for it to complete. This isn't an exception; it's been more like the rule since over a year now.

Now confessedly, it's a big table (~75M rows). The hardware it's operating on has 16 cores and 120 GB memory. I've been monitoring the server's performance – there's no bottleneck there, far from it.

Look at the the explain analyze results here: https://explain.depesz.com/s/ATwE It seems time is eaten up by a sequential scan.

Moreover here's the output of\d links_publicreply:

                                      Table "public.links_publicreply"
     Column      |           Type           |                           Modifiers                            
-----------------+--------------------------+----------------------------------------------------------------
 id              | integer                  | not null default nextval('links_publicreply_id_seq'::regclass)
 submitted_by_id | integer                  | not null
 answer_to_id    | integer                  | not null
 submitted_on    | timestamp with time zone | not null
 description     | text                     | not null
 category        | character varying(20)    | not null
 seen            | boolean                  | not null
 abuse           | boolean                  | not null
 device          | character varying(10)    | default '1'::character varying
Indexes:
    "links_publicreply_pkey" PRIMARY KEY, btree (id)
    "links_publicreply_answer_to_id" btree (answer_to_id)
    "links_publicreply_submitted_by_id" btree (submitted_by_id)
Foreign-key constraints:
    "links_publicreply_answer_to_id_fkey" FOREIGN KEY (answer_to_id) REFERENCES links_link(id) DEFERRABLE INITIALLY DEFERRED
    "links_publicreply_submitted_by_id_fkey" FOREIGN KEY (submitted_by_id) REFERENCES auth_user(id) DEFERRABLE INITIALLY DEFERRED
Referenced by:
    TABLE "links_report" CONSTRAINT "links_report_which_publicreply_id_fkey" FOREIGN KEY (which_publicreply_id) REFERENCES links_publicreply(id) DEFERRABLE INITIALLY DEFERRED
    TABLE "links_seen" CONSTRAINT "links_seen_which_reply_id_fkey" FOREIGN KEY (which_reply_id) REFERENCES links_publicreply(id) DEFERRABLE INITIALLY DEFERRED
    TABLE "links_link" CONSTRAINT "publicreplyposter_link_fkey" FOREIGN KEY (latest_reply_id) REFERENCES links_publicreply(id) ON UPDATE CASCADE ON DELETE CASCADE

Is there any way I could have performed a query like this differently? I need to perform maintenance on this table – but the times are exorbitant. Please advise on all options (if any) I have here.

In case it matters, also adding the output for \d links_link here:

                                         Table "public.links_link"
        Column        |           Type           |                        Modifiers                        
----------------------+--------------------------+---------------------------------------------------------
 id                   | integer                  | not null default nextval('links_link_id_seq'::regclass)
 description          | text                     | not null
 submitter_id         | integer                  | not null
 submitted_on         | timestamp with time zone | not null
 rank_score           | double precision         | not null
 url                  | character varying(250)   | not null
 cagtegory            | character varying(25)    | not null
 image_file           | character varying(100)   | 
 reply_count          | integer                  | default 0
 device               | character varying(10)    | default '1'::character varying
 latest_reply_id      | integer                  | 
 which_photostream_id | integer                  | 
 is_visible           | boolean                  | default true
 net_votes            | integer                  | default 0
Indexes:
    "links_link_pkey" PRIMARY KEY, btree (id)
    "links_link_submitter_id" btree (submitter_id)
Foreign-key constraints:
    "link_whichphotostreamid_fkey" FOREIGN KEY (which_photostream_id) REFERENCES links_photostream(id) ON UPDATE CASCADE ON DELETE CASCADE
    "links_link_submitter_id_fkey" FOREIGN KEY (submitter_id) REFERENCES auth_user(id) DEFERRABLE INITIALLY DEFERRED
    "publicreplyposter_link_fkey" FOREIGN KEY (latest_reply_id) REFERENCES links_publicreply(id) ON UPDATE CASCADE ON DELETE CASCADE
Referenced by:
    TABLE "links_publicreply" CONSTRAINT "links_publicreply_answer_to_id_fkey" FOREIGN KEY (answer_to_id) REFERENCES links_link(id) DEFERRABLE INITIALLY DEFERRED
    TABLE "links_report" CONSTRAINT "links_report_which_link_id_fkey" FOREIGN KEY (which_link_id) REFERENCES links_link(id) DEFERRABLE INITIALLY DEFERRED
    TABLE "links_vote" CONSTRAINT "links_vote_link_id_fkey" FOREIGN KEY (link_id) REFERENCES links_link(id) DEFERRABLE INITIALLY DEFERRED
    TABLE "links_photoobjectsubscription" CONSTRAINT "which_link_id_photoobjectsubscription" FOREIGN KEY (which_link_id) REFERENCES links_link(id) ON DELETE CASCADE

Best Answer

The sequential scan is taking only 23 seconds. The key is to look at the full text of the plan, which shows the missing time:

Trigger for constraint publicreplyposter_link_fkey: time=766392.766 calls=238

(explain.depesz.com doesn't do such a great job with marking up the plans from non-select queries)

So, it looks like you are missing a create index on links_link (latest_reply_id).

That means every row you delete from links_publicreply has to do a full table scan on links_link to make sure it is not referencing that row.

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You write:

Each customer can have multiple sites, but only one should be displayed in this list.

Yet, your query retrieves all rows. That would be a point to optimize. But you also do not define which site is to be picked.

Either way, it does not matter much here. Your EXPLAIN shows only 5026 rows for the site scan (5018 for the customer scan). So hardly any customer actually has more than one site. Did you ANALYZE your tables before running EXPLAIN?

From the numbers I see in your EXPLAIN, indexes will give you nothing for this query. Sequential table scans will be the fastest possible way. Half a second is rather slow for 5000 rows, though. Maybe your database needs some general performance tuning?

Maybe the query itself is faster, but "half a second" includes network transfer? EXPLAIN ANALYZE would tell us more.

If this query is your bottleneck, I would suggest you implement a materialized view.

After you provided more information I find that my diagnosis pretty much holds.

The query itself needs 27 ms. Not much of a problem there. "Half a second" was the kind of misunderstanding I had suspected. The slow part is the network transfer (plus ssh encoding / decoding, possibly rendering). You should only retrieve 100 rows, that would solve most of it, even if it means to execute the whole query every time.

If you go the route with a materialized view like I proposed you could add a serial number without gaps to the table plus index on it - by adding a column row_number() OVER (<your sort citeria here>) AS mv_id.

Then you can query:

SELECT *
FROM   materialized_view
WHERE  mv_id >= 2700
AND    mv_id <  2800;

This will perform very fast. LIMIT / OFFSET cannot compete, that needs to compute the whole table before it can sort and pick 100 rows.

pgAdmin timing

When you execute a query from the query tool, the message pane shows something like:

Total query runtime: 62 ms.

And the status line shows the same time. I quote pgAdmin help about that:

The status line will show how long the last query took to complete. If a dataset was returned, not only the elapsed time for server execution is displayed, but also the time to retrieve the data from the server to the Data Output page.

If you want to see the time on the server you need to use SQL EXPLAIN ANALYZE or the built in Shift + F7keyboard shortcut or Query -> Explain analyze. Then, at the bottom of the explain output you get something like this:

Total runtime: 0.269 ms

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Rather than "VARCHAR(40000)" why not use "TEXT"?
HASH index use is discouraged (see docs at http://www.postgresql.org/docs/current/static/indexes-types.html).
Have you run "ANALYZE" on your tables before running the query?
Giant IN lists can be performance killers.

How do the following queries perform?

SELECT e.entityId
FROM entities e
INNER JOIN triples t ON (t.object = e.entityId)
LIMIT 10000;

SELECT e.entityId
FROM entities e
WHERE EXISTS (SELECT 1 FROM triples t WHERE t.object = e.entityId LIMIT 10000);

Best Answer

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