Postgresql – Debug query on big table that is sometimes slow

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I have a web API that is backed by a Postgres database, and the performance is generally very good. I monitor the performance of both the database and the application as a whole. Most of my queries (and API calls for that matter) complete in less than 100ms, however occasionally there's an outlier.

Just today I received an alert that an API call took longer than 5,000ms and was thusly terminated by a watchdog. From digging into the logs the underlying Postgres query took over 13 seconds to complete (everything is asynchronous, so even though the API request was terminated the SQL query continued).

This is very atypical, and even when I run the offending query manually I am unable to reproduce such atrocious timing. It runs to completion in 985ms (according to explain analyze) for me.

My Question

I am not sure what else to look at next to try and formulate theories on why this occurred. It doesn't happen that often, only once or twice a day out of thousands of similar events a day, but it does occur often enough that it's annoying. What am I missing? What next steps should I go down to debug this? I'm not from a DBA background, so this probably is a silly question.

Some quick background & what I've tried

This is all hosted on Amazon's RDS, running Postgres 9.4 on a m3.xlarge, Provisioned IOPS (2,000).

One of my tables, let's call it "details" is rather large, containing nearly 5 millions rows and growing at a rate of 25,000 records a day. This table is never updated or deleted, just inserts and selects, but represents the "core" of my application – most nearly anything of interest is read from this table.

In this specific case, I do know that this query has some parameters (e.g. the dates at the bottom and the ids) such that it's looking at a rather large dataset. I've already developed a much improved version of this query that takes this specific scenario down from 985ms down to 20. However, I am concerned that there's something else "at play" here that a query that takes less than a second to run for me, takes over 13 seconds every now and then in production.

The table

Well, kind of… It contains many more columns, but I stripped out any columns either not in the query or without indexes. All column used in the below query, or with an index attached have been left;

CREATE TABLE "public"."details" (
    "value" numeric,
    "created_at" timestamp(6) WITH TIME ZONE NOT NULL,
    "updated_at" timestamp(6) WITH TIME ZONE NOT NULL,
    "effective_date" timestamp(6) WITH TIME ZONE,
    "submission_date" timestamp(6) WITH TIME ZONE,
    "id" uuid NOT NULL,
    "form_id" uuid,
    "order_id" uuid,
    "invoice_id" uuid,
    "customer_id" uuid,
    "seq" int8 NOT NULL DEFAULT nextval('details_seq_seq'::regclass),
    "client_day" date,
    CONSTRAINT "details_pkey" PRIMARY KEY ("id") NOT DEFERRABLE INITIALLY IMMEDIATE,
    CONSTRAINT "details_id_key" UNIQUE ("id") NOT DEFERRABLE INITIALLY IMMEDIATE
)
WITH (OIDS=FALSE);
ALTER TABLE "public"."details" OWNER TO "user";
CREATE UNIQUE INDEX  "details_id_key" ON "public"."details" USING btree("id" "pg_catalog"."uuid_ops" ASC NULLS LAST);
CREATE INDEX  "details_pkey" ON "public"."details" USING btree("id" "pg_catalog"."uuid_ops" ASC NULLS LAST);
CREATE INDEX  "client_day_details" ON "public"."details" USING btree(client_day "pg_catalog"."date_ops" ASC NULLS LAST);
CREATE INDEX  "created_at_details" ON "public"."details" USING btree(created_at "pg_catalog"."timestamptz_ops" ASC NULLS LAST);
CREATE INDEX  "effective_date_details" ON "public"."details" USING btree(effective_date "pg_catalog"."timestamptz_ops" ASC NULLS LAST);
CREATE INDEX  "form_id_details" ON "public"."details" USING btree(form_id "pg_catalog"."uuid_ops" ASC NULLS LAST);
CREATE INDEX  "order_id_details" ON "public"."details" USING btree(order_id "pg_catalog"."uuid_ops" ASC NULLS LAST);
CREATE INDEX  "customer_id_details" ON "public"."details" USING btree(customer_id "pg_catalog"."uuid_ops" ASC NULLS LAST);
CREATE INDEX  "seq_updated_at_effective_date_details" ON "public"."details" USING btree(seq "pg_catalog"."int8_ops" ASC NULLS LAST, updated_at "pg_catalog"."timestamptz_ops" ASC NULLS LAST, effective_date "pg_catalog"."timestamptz_ops" ASC NULLS LAST);
ALTER TABLE "public"."details" CLUSTER ON "seq_updated_at_effective_date_details";
CREATE INDEX  "invoice_id_details" ON "public"."details" USING btree(invoice_id "pg_catalog"."uuid_ops" ASC NULLS LAST);
CREATE INDEX  "updated_attribute_vals" ON "public"."details" USING btree(updated_at "pg_catalog"."timestamptz_ops" ASC NULLS LAST);

The query

SELECT
    "count_pages"(
        array_to_json(array_agg(t)),
        '{"limit":500,"mode":"u"}'
    ) :: text as json
from
    (
        SELECT
            "t1"."seq"
        FROM
            (
                (
                    "details" "t1"
                    JOIN "orders" "j1" ON "j1"."id" = "t1"."order_id"
                )
                JOIN "invoices" "j2" ON "j2"."id" = "j1"."invoice_id"
            )
        JOIN "accounts" "j3" ON "j3"."id" = "j2"."account_id"
        WHERE
            (
                "j3"."customer_id" = '3e6ec3ac-fcce-4698-b1a6-87140e1197ec'
                AND "j3"."id" = ANY(
                    '{"9ee9979d-bd3f-40fd-932a-b7e3c1a4b046", "a1a695f3-eee5-4654-a5f5-967192a5781b", "0b118f5e-d1a8-42d4-8c1f-719180a44b89"}'
                )
            )
        AND(
            "t1"."effective_date" >= '2016-01-28T14:56:31.000Z'
            AND "t1"."updated_at" >= '2016-02-07T21:29:50.000Z'
        )
        ORDER BY
            "t1"."seq" ASC
    ) t

`EXPLAIN ANALYZE`

Aggregate  (cost=23500.37..23500.63 rows=1 width=32) (actual time=985.927..985.928 rows=1 loops=1)
  ->  Subquery Scan on t  (cost=23499.87..23500.28 rows=33 width=32) (actual time=940.274..962.487 rows=7166 loops=1)
        ->  Sort  (cost=23499.87..23499.95 rows=33 width=8) (actual time=940.248..947.794 rows=7166 loops=1)
              Sort Key: t1.seq
              Sort Method: quicksort  Memory: 528kB
              ->  Nested Loop  (cost=5.19..23499.04 rows=33 width=8) (actual time=1.964..929.479 rows=7166 loops=1)
                    ->  Nested Loop  (cost=4.76..193.87 rows=182 width=16) (actual time=0.293..11.758 rows=854 loops=1)
                          ->  Nested Loop  (cost=4.47..74.20 rows=24 width=16) (actual time=0.210..1.294 rows=85 loops=1)
                                ->  Seq Scan on accounts j3  (cost=0.00..6.64 rows=1 width=16) (actual time=0.074..0.132 rows=3 loops=1)
                                      Filter: ((customer_id = '3e6ec3ac-fcce-4698-b1a6-87140e1197ec'::uuid) AND (id = ANY ('{9ee9979d-bd3f-40fd-932a-b7e3c1a4b046,a1a695f3-eee5-4654-a5f5-967192a5781b,0b118f5e-d1a8-42d4-8c1f-719180a44b89}'::uuid[])))
                                      Rows Removed by Filter: 102
                                ->  Bitmap Heap Scan on invoices j2  (cost=4.47..67.31 rows=25 width=32) (actual time=0.062..0.294 rows=28 loops=3)
                                      Recheck Cond: (account_id = j3.id)
                                      Heap Blocks: exact=64
                                      ->  Bitmap Index Scan on account_id_invoices  (cost=0.00..4.47 rows=25 width=0) (actual time=0.043..0.043 rows=28 loops=3)
                                            Index Cond: (account_id = j3.id)
                          ->  Index Scan using invoice_id_orders on orders j1  (cost=0.29..4.91 rows=8 width=32) (actual time=0.020..0.098 rows=10 loops=85)
                                Index Cond: (invoice_id = j2.id)
                    ->  Index Scan using order_id_details on details t1  (cost=0.43..128.04 rows=1 width=24) (actual time=0.054..1.054 rows=8 loops=854)
                          Index Cond: (order_id = j1.id)
                          Filter: ((effective_date >= '2016-01-28 14:56:31+00'::timestamp with time zone) AND (updated_at >= '2016-02-07 21:29:50+00'::timestamp with time zone))
                          Rows Removed by Filter: 494
Planning time: 5.103 ms
Execution time: 986.798 ms

`EXPLAIN (ANALYZE, BUFFERS)`

Aggregate  (cost=23500.68..23500.95 rows=1 width=32) (actual time=332.305..332.306 rows=1 loops=1)
  Buffers: shared hit=246886
  ->  Subquery Scan on t  (cost=23500.18..23500.60 rows=33 width=32) (actual time=289.528..315.790 rows=8413 loops=1)
        Buffers: shared hit=246886
        ->  Sort  (cost=23500.18..23500.27 rows=33 width=8) (actual time=289.507..298.363 rows=8413 loops=1)
              Sort Key: t1.seq
              Sort Method: quicksort  Memory: 779kB
              Buffers: shared hit=246886
              ->  Nested Loop  (cost=5.19..23499.35 rows=33 width=8) (actual time=0.275..277.738 rows=8413 loops=1)
                    Buffers: shared hit=246886
                    ->  Nested Loop  (cost=4.76..193.87 rows=182 width=16) (actual time=0.091..5.067 rows=854 loops=1)
                          Buffers: shared hit=1115
                          ->  Nested Loop  (cost=4.47..74.20 rows=24 width=16) (actual time=0.076..0.566 rows=85 loops=1)
                                Buffers: shared hit=77
                                ->  Seq Scan on accounts j3  (cost=0.00..6.64 rows=1 width=16) (actual time=0.038..0.065 rows=3 loops=1)
                                      Filter: ((customer_id = '3e6ec3ac-fcce-4698-b1a6-87140e1197ec'::uuid) AND (id = ANY ('{9ee9979d-bd3f-40fd-932a-b7e3c1a4b046,a1a695f3-eee5-4654-a5f5-967192a5781b,0b118f5e-d1a8-42d4-8c1f-719180a44b89}'::uuid[])))
                                      Rows Removed by Filter: 102
                                      Buffers: shared hit=5
                                ->  Bitmap Heap Scan on invoices j2  (cost=4.47..67.31 rows=25 width=32) (actual time=0.025..0.090 rows=28 loops=3)
                                      Recheck Cond: (account_id = j3.id)
                                      Heap Blocks: exact=64
                                      Buffers: shared hit=72
                                      ->  Bitmap Index Scan on account_id_invoices  (cost=0.00..4.47 rows=25 width=0) (actual time=0.016..0.016 rows=28 loops=3)
                                            Index Cond: (account_id = j3.id)
                                            Buffers: shared hit=8
                          ->  Index Scan using invoice_id_orders on orders j1  (cost=0.29..4.91 rows=8 width=32) (actual time=0.006..0.029 rows=10 loops=85)
                                Index Cond: (invoice_id = j2.id)
                                Buffers: shared hit=1038
                    ->  Index Scan using order_id_details on details t1  (cost=0.43..128.04 rows=1 width=24) (actual time=0.015..0.296 rows=10 loops=854)
                          Index Cond: (order_id = j1.id)
                          Filter: ((effective_date >= '2016-01-28 14:56:31+00'::timestamp with time zone) AND (updated_at >= '2016-02-07 21:29:50+00'::timestamp with time zone))
                          Rows Removed by Filter: 494
                          Buffers: shared hit=245771
Planning time: 0.897 ms
Execution time: 333.020 ms

Here are some graphs/charts from during the "event";

RDS

New Relic

Best Answer

Table definition

A low hanging fruit first: The UNIQUE constraint details_id_key is a total waste of resources. It adds nothing useful over the existing PK details_pkey.

Where did you get these noisy DDL statements? All the redundant default clauses cloud the view. After trimming the noise:

CREATE TABLE public.details (
   value numeric,
   created_at timestamptz NOT NULL,
   updated_at timestamptz NOT NULL,
   effective_date timestamptz,
   submission_date timestamptz,
   id uuid NOT NULL,
   form_id uuid,
   order_id uuid,
   invoice_id uuid,
   customer_id uuid,
   seq int8 NOT NULL DEFAULT nextval('details_seq_seq'::regclass),
   client_day date,
   CONSTRAINT details_pkey PRIMARY KEY (id),
   CONSTRAINT details_id_key UNIQUE (id)  -- total waste
);

Query

I would have a couple of things to say to your query:

Use json_agg(t) instead of array_to_json(array_agg(t))?
Why join to orders at all? Can you join invoices to details directly?
```
JOIN invoices j2 ON j2.id = t1.invoice_id
```

Then I would ask for the definition of count_pages() (in your question) and for other details. But given your statement:

I've already developed a much improved version of this query that takes this specific scenario down from 985ms down to 20.

... I might be just wasting time. Rather have a separate question based on your improved version of the query - if you still need it.

Query plan gone wrong

Most of the total time is spent in one of the nested loop steps, where Postgres bases the plan on seriously underestimated row counts in both query plans:

   ->  Nested Loop  (cost=5.19..23499.04 rows=33 width=8)
             (actual time=1.964..929.479 rows=7166 loops=1)

   ->  Nested Loop  (cost=5.19..23499.35 rows=33 width=8)
             (actual time=0.275..277.738 rows=8413 loops=1)

That's the join between details and orders. _{(I am not even convinced you need orders in the query at all.)} The low estimates also build up in every step that leads up to this nested loop.

If Postgres would know to expect that many rows, it would probably choose a merge join or hash join instead.

The number of actual rows has grown in your second query plan, while the estimate has not. This would indicate that you are not running ANALYZE enough or that you just had big INSERTs adding more data and that's not reflected in the table statistics, yet. These two predicates in your query are typical suspects for such a situation:

AND t1.effective_date >= '2016-01-28T14:56:31.000Z'
AND t1.updated_at     >= '2016-02-07T21:29:50.000Z'

I would guess you add newer rows all the time, your autovacuum isn't keeping up with the latest stats on the newest rows while your query focuses on just those rows. This can escalate over time or after particularly big INSERTs.

Statistics for your big table

autovacuum is based on a percentage of rows inserted / updated / deleted. Default settings can be a bit of a trap for your special situation: a big table growing at a constant rate. Especially when mostly the latest additions are relevant for your query.

5M rows, 25K new rows per day. After 10 days, autovacuum "reckons":
Only 5 % new rows, my default autovacuum_analyze_scale_factor is 10 %. No need to run ANALYZE

The manual:

autovacuum_analyze_scale_factor (floating point)

Specifies a fraction of the table size to add to autovacuum_analyze_threshold when deciding whether to trigger an ANALYZE. The default is 0.1 (10% of table size). This parameter can only be set in the postgresql.conf file or on the server command line; but the setting can be overridden for individual tables by changing table storage parameters.

Bold emphasis mine. Read about the other autovacuum setting, too!

I suggest more aggressive settings - at least for your all-important table details. Per-table settings are possible:

It is possible to run ANALYZE on specific tables and even just specific columns of a table, so the flexibility exists to update some statistics more frequently than others if your application requires it.

Use Storage Parameters for your table. Example:

ALTER TABLE public.details SET (autovacuum_analyze_scale_factor = 0.001);

When is Postgres autovacuum executed

And run ANALYZE manually after big INSERTs with new data, before following up immediately with a (possibly) expensive query involving those newly added rows. Quoting the manual once more:

We recommend that active production databases be vacuumed frequently (at least nightly), in order to remove dead rows. After adding or deleting a large number of rows, it might be a good idea to issue a VACUUM ANALYZE command for the affected table. This will update the system catalogs with the results of all recent changes, and allow the PostgreSQL query planner to make better choices in planning queries.

Index

Less importantly, I would also consider a multicolumn index:

CREATE INDEX details_order_id_timestamps ON public.details
   (order_id, effective_date DESC NULLS LAST, updated_at DESC NULLS LAST);

I also do not see any index-only scans, which can also point towards VACUUM not running enough (compare the manual here) or that there are no covering indexes, or both. It might pay to review which of your many indexes are actually used and which might be missing.

My Question

Some quick background & what I've tried

The table

The query

EXPLAIN ANALYZE

EXPLAIN (ANALYZE, BUFFERS)

RDS

New Relic

Best Answer

Table definition

Query

Query plan gone wrong

Statistics for your big table

Index

Related Solutions

Postgresql – How to speed up a Postgres query containing lots of Joins with an ILIKE condition

Postgresql – postgres explain plan with giant gaps between operations

Related Question

`EXPLAIN ANALYZE`

`EXPLAIN (ANALYZE, BUFFERS)`