Batch iteration in a tree hierarchy (proof of concept)
The group hierarchy in GitLab is represented with a tree, where the root element
is the top-level namespace, and the child elements are the subgroups or the
recently introduced Namespaces::ProjectNamespace records.
The tree is implemented in the namespaces table ,via the parent_id column.
The column points to the parent namespace record. The top level namespace has no
parent_id.
Partial hierarchy of gitlab-org:
Efficiently iterating over the group hierarchy has several potential use cases. This is true especially in background jobs, which need to perform queries on the group hierarchy, where stable and safe execution is more important than fast runtime. Batch iteration requires more network round-trips, but each batch provides similar performance characteristics.
A few examples:
- For each subgroup, do something.
- For each project in the hierarchy, do something.
- For each issue in the hierarchy, do something.
Problem statement
A group hierarchy could grow so big that a single query would not be able to load it in time. The query would fail with statement timeout error.
Addressing scalability issues related to very large groups requires us to store the same data in different formats (de-normalization). However, if we’re unable to load the group hierarchy, then de-normalization could not be implemented.
One de-normalization technique would be to store all descendant group IDs for a given group. This would speed up queries where we need to load the group and its subgroups. Example:
| GROUP_ID | DESCENDANT_GROUP_IDS |
|---|---|
| 1 |
[2,3,4]
|
| 2 |
[]
|
| 3 |
[4]
|
| 4 |
[]
|
With this structure, determining all the subgroups would require us to read only one row from the database, instead of 4 rows. For a hierarchy as big as 1000 groups, this could make a huge difference.
The reading of the hierarchy problem is solved with this de-normalization. However, we still need to find a way to persist this data in a table. Because a group and its hierarchy could grow very large, we cannot expect a single query to work here.
SELECT id FROM namespaces WHERE traversal_ids && ARRAY[9970]
The query above could time out for large groups, so we need to process the data in batches.
Implementing batching logic in a tree is not something we’ve looked at before,
and it’s fairly complex to implement. An EachBatch or find_in_batches based
solution would not work because:
- The data (group IDs) are not sorted in the hierarchy.
- Groups in subgroups don’t know about the top-level group ID.
Algorithm
The batching query is implemented as a recursive CTE SQL query, where one batch would read a maximum of N rows. Due to the tree structure, reading N rows might not necessarily mean that we’re reading N group IDs. If the tree is structured in a non-optimal way, a batch could return less (but never more) group IDs.
The query implements a depth-first tree walking logic, where the DB scans the first branch of the tree until the leaf element. We’re implementing depth-first algorithm because, when a batch is finished, the query must return enough information for the next batch (cursor). In GitLab, we limit the depth of the tree to 20, which means that in the worst case, the query would return a cursor containing 19 elements.
Implementing a breadth-first tree walking algorithm would be impractical, because a group can have unbounded number of descendants, thus we might end up with a huge cursor.
- Create an initializer row that contains:
- The currently processed group ID (top-level group ID)
- Two arrays (tree depth and the collected IDs)
- A counter for tracking the number of row reads in the query.
- Recursively process the row and do one of the following (whenever the condition matches):
- Load the first child namespace and update the currently processed namespace ID if we’re not at the leaf node. (Walking down a branch)
- Load the next namespace record on the current depth if there are any rows left.
- Walk up one node and process rows at one level higher.
- Continue the processing until the number of reads reaches our
LIMIT(batch size). - Find the last processed row which contains the data for the cursor, and all the collected record IDs.
WITH RECURSIVE result AS (
(
SELECT
9970 AS current_id, /* current namespace id we're processing */
ARRAY[9970]::int[] AS depth, /* cursor */
ARRAY[9970]::int[] AS ids, /* collected ids */
1::bigint AS reads,
'initialize' AS action
) UNION ALL
(
WITH cte AS ( /* trick for referencing the result cte multiple times */
select * FROM result
)
SELECT * FROM (
(
SELECT /* walk down the branch */
namespaces.id,
cte.depth || namespaces.id,
cte.ids || namespaces.id,
cte.reads + 1,
'walkdown'
FROM namespaces, cte
WHERE
namespaces.parent_id = cte.current_id
ORDER BY namespaces.id ASC
LIMIT 1
) UNION ALL
(
SELECT /* find next element on the same level */
namespaces.id,
cte.depth[:array_length(cte.depth, 1) - 1] || namespaces.id,
cte.ids || namespaces.id,
cte.reads + 1,
'next'
FROM namespaces, cte
WHERE
namespaces.parent_id = cte.depth[array_length(cte.depth, 1) - 1] AND
namespaces.id > cte.depth[array_length(cte.depth, 1)]
ORDER BY namespaces.id ASC
LIMIT 1
) UNION ALL
(
SELECT /* jump up one node when finished with the current level */
cte.current_id,
cte.depth[:array_length(cte.depth, 1) - 1],
cte.ids,
cte.reads + 1,
'jump'
FROM cte
WHERE cte.depth <> ARRAY[]::int[]
LIMIT 1
)
) next_row LIMIT 1
)
)
SELECT current_id, depth, ids, action
FROM result
current_id | depth | ids | action
------------+--------------+------------------------+------------
24 | {24} | {24} | initialize
25 | {24,25} | {24,25} | walkdown
26 | {24,26} | {24,25,26} | next
112 | {24,112} | {24,25,26,112} | next
113 | {24,113} | {24,25,26,112,113} | next
114 | {24,113,114} | {24,25,26,112,113,114} | walkdown
114 | {24,113} | {24,25,26,112,113,114} | jump
114 | {24} | {24,25,26,112,113,114} | jump
114 | {} | {24,25,26,112,113,114} | jump
self_and_descendants implementation
based on the traversal_ids column. The query above should be only used when
implementing batch iteration over the group hierarchy.Rudimentary batching implementation in Ruby:
class NamespaceEachBatch
def initialize(namespace_id:, cursor: nil)
@namespace_id = namespace_id
@cursor = cursor || { current_id: namespace_id, depth: [namespace_id] }
end
def each_batch(of: 500)
current_cursor = cursor.dup
first_iteration = true
loop do
new_cursor, ids = load_batch(cursor: current_cursor, of: of, first_iteration: first_iteration)
first_iteration = false
current_cursor = new_cursor
yield ids
break if new_cursor[:depth].empty?
end
end
private
# yields array of namespace ids
def load_batch(cursor:, of:, first_iteration: false)
recursive_cte = Gitlab::SQL::RecursiveCTE.new(:result,
union_args: { remove_order: false, remove_duplicates: false })
ids = first_iteration ? namespace_id.to_s : ""
recursive_cte << Namespace.select(
Arel.sql(Integer(cursor.fetch(:current_id)).to_s).as('current_id'),
Arel.sql("ARRAY[#{cursor.fetch(:depth).join(',')}]::int[]").as('depth'),
Arel.sql("ARRAY[#{ids}]::int[]").as('ids'),
Arel.sql("1::bigint AS count")
).from('(VALUES (1)) AS does_not_matter').limit(1)
cte = Gitlab::SQL::CTE.new(:cte, Namespace.select('*').from('result'))
union_query = Namespace.with(cte.to_arel).from_union(
walk_down,
next_elements,
up_one_level,
remove_duplicates: false,
remove_order: false
).select('current_id', 'depth', 'ids', 'count').limit(1)
recursive_cte << union_query
scope = Namespace.with
.recursive(recursive_cte.to_arel)
.from(recursive_cte.alias_to(Namespace.arel_table))
.limit(of)
row = Namespace.from(scope.arel.as('namespaces')).order(count: :desc).limit(1).first
[
{ current_id: row[:current_id], depth: row[:depth] },
row[:ids]
]
end
attr_reader :namespace_id, :cursor
def walk_down
Namespace.select(
Arel.sql('namespaces.id').as('current_id'),
Arel.sql('cte.depth || namespaces.id').as('depth'),
Arel.sql('cte.ids || namespaces.id').as('ids'),
Arel.sql('cte.count + 1').as('count')
).from('cte, LATERAL (SELECT id FROM namespaces WHERE parent_id = cte.current_id ORDER BY id LIMIT 1) namespaces')
end
def next_elements
Namespace.select(
Arel.sql('namespaces.id').as('current_id'),
Arel.sql('cte.depth[:array_length(cte.depth, 1) - 1] || namespaces.id').as('depth'),
Arel.sql('cte.ids || namespaces.id').as('ids'),
Arel.sql('cte.count + 1').as('count')
).from('cte, LATERAL (SELECT id FROM namespaces WHERE namespaces.parent_id = cte.depth[array_length(cte.depth, 1) - 1] AND namespaces.id > cte.depth[array_length(cte.depth, 1)] ORDER BY id LIMIT 1) namespaces')
end
def up_one_level
Namespace.select(
Arel.sql('cte.current_id').as('current_id'),
Arel.sql('cte.depth[:array_length(cte.depth, 1) - 1]').as('depth'),
Arel.sql('cte.ids').as('ids'),
Arel.sql('cte.count + 1').as('count')
).from('cte')
.where('cte.depth <> ARRAY[]::int[]')
.limit(1)
end
end
iterator = NamespaceEachBatch.new(namespace_id: 9970)
all_ids = []
iterator.each_batch do |ids|
all_ids.concat(ids)
end
# Test
puts all_ids.count
puts all_ids.sort == Namespace.where('traversal_ids && ARRAY[9970]').pluck(:id).sort
Example batch query:
SELECT
"namespaces".*
FROM ( WITH RECURSIVE "result" AS ((
SELECT
15847356 AS current_id,
ARRAY[9970,
12061481,
12128714,
12445111,
15847356]::int[] AS depth,
ARRAY[]::int[] AS ids,
1::bigint AS count
FROM (
VALUES (1)) AS does_not_matter
LIMIT 1)
UNION ALL ( WITH "cte" AS MATERIALIZED (
SELECT
*
FROM
result
)
SELECT
current_id,
depth,
ids,
count
FROM ((
SELECT
namespaces.id AS current_id,
cte.depth || namespaces.id AS depth,
cte.ids || namespaces.id AS ids,
cte.count + 1 AS count
FROM
cte,
LATERAL (
SELECT
id
FROM
namespaces
WHERE
parent_id = cte.current_id
ORDER BY
id
LIMIT 1
) namespaces
)
UNION ALL (
SELECT
namespaces.id AS current_id,
cte.depth[:array_length(
cte.depth, 1
) - 1] || namespaces.id AS depth,
cte.ids || namespaces.id AS ids,
cte.count + 1 AS count
FROM
cte,
LATERAL (
SELECT
id
FROM
namespaces
WHERE
namespaces.parent_id = cte.depth[array_length(
cte.depth, 1
) - 1]
AND namespaces.id > cte.depth[array_length(
cte.depth, 1
)]
ORDER BY
id
LIMIT 1
) namespaces
)
UNION ALL (
SELECT
cte.current_id AS current_id,
cte.depth[:array_length(
cte.depth, 1
) - 1] AS depth,
cte.ids AS ids,
cte.count + 1 AS count
FROM
cte
WHERE (
cte.depth <> ARRAY[]::int[]
)
LIMIT 1
)
) namespaces
LIMIT 1
))
SELECT
"namespaces".*
FROM
"result" AS "namespaces"
LIMIT 500) namespaces
ORDER BY
"count" DESC
LIMIT 1
Execution plan:
Limit (cost=16.36..16.36 rows=1 width=76) (actual time=436.963..436.970 rows=1 loops=1)
Buffers: shared hit=3721 read=423 dirtied=8
I/O Timings: read=412.590 write=0.000
-> Sort (cost=16.36..16.39 rows=11 width=76) (actual time=436.961..436.968 rows=1 loops=1)
Sort Key: namespaces.count DESC
Sort Method: top-N heapsort Memory: 27kB
Buffers: shared hit=3721 read=423 dirtied=8
I/O Timings: read=412.590 write=0.000
-> Limit (cost=15.98..16.20 rows=11 width=76) (actual time=0.005..436.394 rows=500 loops=1)
Buffers: shared hit=3718 read=423 dirtied=8
I/O Timings: read=412.590 write=0.000
CTE result
-> Recursive Union (cost=0.00..15.98 rows=11 width=76) (actual time=0.003..432.924 rows=500 loops=1)
Buffers: shared hit=3718 read=423 dirtied=8
I/O Timings: read=412.590 write=0.000
-> Limit (cost=0.00..0.01 rows=1 width=76) (actual time=0.002..0.003 rows=1 loops=1)
I/O Timings: read=0.000 write=0.000
-> Result (cost=0.00..0.01 rows=1 width=76) (actual time=0.001..0.002 rows=1 loops=1)
I/O Timings: read=0.000 write=0.000
-> Limit (cost=0.76..1.57 rows=1 width=76) (actual time=0.862..0.862 rows=1 loops=499)
Buffers: shared hit=3718 read=423 dirtied=8
I/O Timings: read=412.590 write=0.000
CTE cte
-> WorkTable Scan on result (cost=0.00..0.20 rows=10 width=76) (actual time=0.000..0.000 rows=1 loops=499)
I/O Timings: read=0.000 write=0.000
-> Append (cost=0.56..17.57 rows=21 width=76) (actual time=0.862..0.862 rows=1 loops=499)
Buffers: shared hit=3718 read=423 dirtied=8
I/O Timings: read=412.590 write=0.000
-> Nested Loop (cost=0.56..7.77 rows=10 width=76) (actual time=0.675..0.675 rows=0 loops=499)
Buffers: shared hit=1693 read=357 dirtied=1
I/O Timings: read=327.812 write=0.000
-> CTE Scan on cte (cost=0.00..0.20 rows=10 width=76) (actual time=0.001..0.001 rows=1 loops=499)
I/O Timings: read=0.000 write=0.000
-> Limit (cost=0.56..0.73 rows=1 width=4) (actual time=0.672..0.672 rows=0 loops=499)
Buffers: shared hit=1693 read=357 dirtied=1
I/O Timings: read=327.812 write=0.000
-> Index Only Scan using index_namespaces_on_parent_id_and_id on public.namespaces namespaces_1 (cost=0.56..5.33 rows=29 width=4) (actual time=0.671..0.671 rows=0 loops=499)
Index Cond: (namespaces_1.parent_id = cte.current_id)
Heap Fetches: 7
Buffers: shared hit=1693 read=357 dirtied=1
I/O Timings: read=327.812 write=0.000
-> Nested Loop (cost=0.57..9.45 rows=10 width=76) (actual time=0.208..0.208 rows=1 loops=442)
Buffers: shared hit=2025 read=66 dirtied=7
I/O Timings: read=84.778 write=0.000
-> CTE Scan on cte cte_1 (cost=0.00..0.20 rows=10 width=72) (actual time=0.000..0.000 rows=1 loops=442)
I/O Timings: read=0.000 write=0.000
-> Limit (cost=0.57..0.89 rows=1 width=4) (actual time=0.203..0.203 rows=1 loops=442)
Buffers: shared hit=2025 read=66 dirtied=7
I/O Timings: read=84.778 write=0.000
-> Index Only Scan using index_namespaces_on_parent_id_and_id on public.namespaces namespaces_2 (cost=0.57..3.77 rows=10 width=4) (actual time=0.201..0.201 rows=1 loops=442)
Index Cond: ((namespaces_2.parent_id = (cte_1.depth)[(array_length(cte_1.depth, 1) - 1)]) AND (namespaces_2.id > (cte_1.depth)[array_length(cte_1.depth, 1)]))
Heap Fetches: 35
Buffers: shared hit=2025 read=66 dirtied=6
I/O Timings: read=84.778 write=0.000
-> Limit (cost=0.00..0.03 rows=1 width=76) (actual time=0.003..0.003 rows=1 loops=59)
I/O Timings: read=0.000 write=0.000
-> CTE Scan on cte cte_2 (cost=0.00..0.29 rows=9 width=76) (actual time=0.002..0.002 rows=1 loops=59)
Filter: (cte_2.depth <> '{}'::integer[])
Rows Removed by Filter: 0
I/O Timings: read=0.000 write=0.000
-> CTE Scan on result namespaces (cost=0.00..0.22 rows=11 width=76) (actual time=0.005..436.240 rows=500 loops=1)
Buffers: shared hit=3718 read=423 dirtied=8
I/O Timings: read=412.590 write=0.000