Very slow query performance in aws postgresql for a table with 4 billion rows

Question

The Problem

We have a relational table where we store user activity. A query like the following takes 77 seconds!

FROM "site_activity"
WHERE
    (
        NOT "site_activity"."is_deleted"
        AND "site_activity"."user_id" = 68812389
        AND NOT (
            "site_activity"."kind" IN (
                'updated',
                'duplicated',
                'reapplied'
            )
        )
        AND NOT (
            "site_activity"."content_type_id" = 14
            AND "site_activity"."kind" = 'created'
        )
    )
ORDER BY
    "site_activity"."created_at" DESC,
    "site_activity"."id" DESC
LIMIT  9;

The query plan looks like this

                                     QUERY PLAN
--------------------------------------------------------------------------------------------
Limit
    (cost=17750.72..27225.75 rows=9 width=16)
    (actual time=199501.336..199501.338 rows=9 loops=1)
  Output: id, created_at
  Buffers: shared hit=4502362 read=693523 written=37273
  I/O Timings: read=190288.205 write=446.870
  ->  Incremental Sort
      (cost=17750.72..2003433582.97 rows=1902974 width=16)
      (actual time=199501.335..199501.336 rows=9 loops=1)
        Output: id, created_at
        Sort Key: site_activity.created_at DESC, site_activity.id DESC
        Presorted Key: site_activity.created_at
        Full-sort Groups: 1  Sort Method: quicksort  Average Memory: 25kB  Peak Memory: 25kB
        Buffers: shared hit=4502362 read=693523 written=37273
        I/O Timings: read=190288.205 write=446.870
        ->  Index Scan Backward using site_activity_created_at_company_id_idx on public.site_activity
            (cost=0.58..2003345645.30 rows=1902974 width=16)
            (actual time=198971.283..199501.285 rows=10 loops=1)
              Output: id, created_at
              Filter: (
                (NOT site_activity.is_deleted) AND (site_activity.user_id = 68812389)
                AND ((site_activity.kind)::text <> ALL ('{updated,duplicated,reapplied}'::text[]))
                AND ((site_activity.content_type_id <> 14) OR ((site_activity.kind)::text <> 'created'::text))
              )
              Rows Removed by Filter: 14735308
              Buffers: shared hit=4502353 read=693523 written=37273
              I/O Timings: read=190288.205 write=446.870
Settings: effective_cache_size = '261200880kB',
          effective_io_concurrency = '400',
          jit = 'off',
          max_parallel_workers = '24',
          random_page_cost = '1.5',
          work_mem = '64MB'
Planning:
  Buffers: shared hit=344
Planning Time: 6.429 ms
Execution Time: 199501.365 ms
(22 rows)

Time: 199691.997 ms (03:19.692)

Table Facts

1. It contains a little more than 4 billion rows.

2. The table structure is

                                               Table "public.site_activity"
       Column      |           Type           | Collation | Nullable |                   Default
   ----------------+--------------------------+-----------+----------+----------------------------------------------
   id              | bigint                   |           | not null | nextval('site_activity_id_seq'::regclass)
   created_at      | timestamp with time zone |           | not null |
   modified_at     | timestamp with time zone |           | not null |
   is_deleted      | boolean                  |           | not null |
   object_id       | bigint                   |           | not null |
   kind            | character varying(32)    |           | not null |
   context         | text                     |           | not null |
   company_id      | integer                  |           | not null |
   content_type_id | integer                  |           | not null |
   user_id         | integer                  |           |          |
   Indexes:
       "site_activity_pkey" PRIMARY KEY, btree (id)
       "site_activity_modified_at_idx" btree (modified_at)
       "site_activity_company_id_idx" btree (company_id)
       "site_activity_created_at_company_id_idx" btree (created_at, company_id)
       "site_activity_object_id_idx" btree (object_id)
       "site_activity_content_type_id_idx" btree (content_type_id)
       "site_activity_kind_idx" btree (kind)
       "site_activity_kind_idx1" btree (kind varchar_pattern_ops)
       "site_activity_user_id_idx" btree (user_id)
   Foreign-key constraints:
       "site_activity_company_id_fk_site_company_id" FOREIGN KEY (company_id)
           REFERENCES site_company(id) DEFERRABLE INITIALLY DEFERRED
       "site_activity_content_type_id_fk_django_co" FOREIGN KEY (content_type_id)
           REFERENCES django_content_type(id) DEFERRABLE INITIALLY DEFERRED
       "site_activity_user_id_fk_site_user_id" FOREIGN KEY (user_id)
           REFERENCES site_user(id) DEFERRABLE INITIALLY DEFERRED
   

   a. kind is treated as an enum. In db we store it as varchar. But in the application (python) we treat it as enum. So the values are fixed. There are around 100 values in it.

   b.content_type_id has around 80 values.

3. This is the distribution of values,

   a. context is actually JSON with a max 8Mb size.

   a. 3 content_type_id values holds 92% of the rows. They are 14 and 19.

   a. 3 kind consumes 75% rows. These are created, updated and sent.

   a. The combination of kind and content_type_id creates 460 values. Among them, 1 combination contains 35% of rows and we exclude them in the query all time.

4. The replica instance has type db.r5.12xlarge. 24 cores, 48 vCPUs, 384GB Mem, storage type io1.

Question

1. How do we handle if the table grows to 100 billion? In the current projection, this can happen in the next 3-5 years.
2. Is NoSQL a good solution? Note we are not accessing the documents with only id or kind.

Notes

1. The facts that I presented might bias the solution to replication in the same host and then later sharding over multiple hosts. But if there is some other solution that can keep up to the 100 billion mark, we should be good.
2. We don't have to use AWS. But preferred.

Answer 1

The current plan is to scan the rows already ordered by "created_at" (using an index) and then stop once it finds 10 (plus maybe a few rows to account for ties) passing the rest of of the conditions. It thinks it will do this very quickly, after only about 1/73,000 of the table (27225.75 / 2003433582.97). but in fact it had to scan much more than that (14735308 / 4000000000, or 1/270 of the table). So it grossly misestimated that part. I don't know if it misestimated it because the number of rows meeting the conditions was estimated incorrectly (It thought there would be 1902974, we don't know how many there actually were, since it stopped early and so stopped counting them) or because it assumed the matching rows would be evenly dispersed over the index, when they were not.

The best index for you will probably be on (user_id, created_at). That way you get to jump to just the part of the index which has the correct user_id (which I assume is where the vast majority of your selectivity comes from) and then still walk that part already in order by "created_at". And you can drop the original index just on (user_id), as the new one will be good for anything that the old one is good for. You could also add "is_deleted" between the other two columns in that index, as it will not spoil the ordering property and will provide some additional selectivity (but probably not much). Any other columns added there will spoil the ordering property, however.

Answer 2

Query

Start by formatting the WHERE clause to make it easier to understand. Comes down to:

FROM   site_activity s
WHERE  s.user_id = 68812389
AND    NOT s.is_deleted
AND    s.kind <> ALL ('{updated,duplicated,reapplied}'::text[])
AND    (content_type_id <> 14 OR kind <> 'created')
ORDER  BY s.created_at DESC, s.id DESC
LIMIT  9;

Index

You commented you always exclude rows for these two conditions. So this partial, multicolumn index would be the optimum:

CREATE INDEX ON public.site_activity (user_id, created_at, id)
WHERE  NOT is_deleted
AND   (content_type_id <> 14 OR kind <> 'created')

Adding id only makes sense if there are many rows with the same (user_id, created_at). Else drop id from the index.

Excluding large, irrelevant parts of the table from the index can pay for such big indexes. (But you may prevent HOT updates for changes on any of the columns involved in the index, including the ones in the WHERE clause.)

The index can only be used while its filters are an obvious subset of the filters in the query.

Table definition

It would pay to optimize your table definition. Like:

    Column      |     Type     | Nullable |                   Default
----------------+--------------+----------+----------------------------------------------
id              | bigint       | not null | nextval('site_activity_id_seq'::regclass)
user_id         | int          | not null |  -- NOT NULL ??
kind            | smallint     | not null |  -- "around 100 values"
content_type_id | smallint     | not null |  -- "around 80 values"
created_at      | timestamptz  | not null |
modified_at     | timestamptz  | not null |
object_id       | bigint       | not null |
company_id      | int          | not null |
is_deleted      | bool         | not null |
context         | text         | not null |

Most importantly, kind now occupies 2 bytes instead of 33 bytes or more. See:

• What is the overhead for varchar(n)?

Plus substantial savings from rearranging the column order. See:

• Calculating and saving space in PostgreSQL

The big column context ("with a max 8Mb size") will typically be stored out-of-line in a TOAST table for most rows, so the tuples to work with shrink to half their size. This makes a difference for most operations.

And I suspect that some of your indexes may be expendable.