kotovalexarian-likes-gitlab/gitlab-org--gitlab-foss

GitLab Bot 78bc39880c Add latest changes from gitlab-org/gitlab@master

2021-12-02 09:10:59 +00:00

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Multiple Databases

To scale GitLab, the we are decomposing the GitLab application database into multiple databases.

CI/CD Database

Support for configuring the GitLab Rails application to use a distinct database for CI/CD tables was introduced in GitLab 14.1. This feature is still under development, and is not ready for production use.

Development setup

By default, GitLab is configured to use only one main database. To opt-in to use a main database, and CI database, modify the config/database.yml file to have a main and a ci database configurations.

You can set this up using GDK or by manually configuring config/database.yml.

GDK configuration

If you are using GDK, you can follow the following steps:

On the GDK root directory, run:

gdk config set gitlab.rails.multiple_databases true

Open your gdk.yml, and confirm that it has the following lines:
```
gitlab:
  rails:
    multiple_databases: true
```
Reconfigure GDK:
```
gdk reconfigure
```
Create the new CI/CD database.

Manually set up the CI/CD database

You can manually edit config/database.yml to split the databases. To do so, consider a config/database.yml file like the example below:

development:
  main:
    adapter: postgresql
    encoding: unicode
    database: gitlabhq_development
    host: /path/to/gdk/postgresql
    pool: 10
    prepared_statements: false
    variables:
      statement_timeout: 120s

test: &test
  main:
    adapter: postgresql
    encoding: unicode
    database: gitlabhq_test
    host: /path/to/gdk/postgresql
    pool: 10
    prepared_statements: false
    variables:
      statement_timeout: 120s

Edit it to split the databases into main and ci:

development:
  main:
    adapter: postgresql
    encoding: unicode
    database: gitlabhq_development
    host: /path/to/gdk/postgresql
    pool: 10
    prepared_statements: false
    variables:
      statement_timeout: 120s
  ci:
    adapter: postgresql
    encoding: unicode
    database: gitlabhq_development_ci
    host: /path/to/gdk/postgresql
    pool: 10
    prepared_statements: false
    variables:
      statement_timeout: 120s

test: &test
  main:
    adapter: postgresql
    encoding: unicode
    database: gitlabhq_test
    host: /path/to/gdk/postgresql
    pool: 10
    prepared_statements: false
    variables:
      statement_timeout: 120s
  ci:
    adapter: postgresql
    encoding: unicode
    database: gitlabhq_test_ci
    host: /path/to/gdk/postgresql
    pool: 10
    prepared_statements: false
    variables:
      statement_timeout: 120s

Next, create the new CI/CD database.

Create the new database

After configuring GitLab for the two databases, create the new CI/CD database:

Create the new ci: database, load the DB schema into the ci: database, and run any pending migrations:
```
bundle exec rails db:create db:schema:load:ci db:migrate
```
Restart GDK:
```
gdk restart
```

Removing joins between `ci_` and non `ci_` tables

Queries that join across databases raise an error. Introduced in GitLab 14.3, for new queries only. Pre-existing queries do not raise an error.

We are planning on moving all the ci_* tables to a separate database, so referencing ci_* tables with other tables will not be possible. This means, that using any kind of JOIN in SQL queries will not work. We have identified already many such examples that need to be fixed in https://gitlab.com/groups/gitlab-org/-/epics/6289 .

Path to removing cross-database joins

The following steps are the process to remove cross-database joins between ci_* and non ci_* tables:

{check-circle} Add all failing specs to the cross-join-allowlist.yml file.
{dotted-circle} Find the code that caused the spec failure and wrap the isolated code in allow_cross_joins_across_databases. Link to a new issue assigned to the correct team to remove the specs from the cross-join-allowlist.yml file.
{dotted-circle} Remove the cross-join-allowlist.yml file and stop allowing whole test files.
{dotted-circle} Fix the problem and remove the allow_cross_joins_across_databases call.
{dotted-circle} Fix all the cross-joins and remove the allow_cross_joins_across_databases method.

Suggestions for removing cross-database joins

The following sections are some real examples that were identified as joining across databases, along with possible suggestions on how to fix them.

Remove the code

The simplest solution we've seen several times now has been an existing scope that is unused. This is the easiest example to fix. So the first step is to investigate if the code is unused and then remove it. These are some real examples:

There may be more examples where the code is used, but we can evaluate if we need it or if the feature should behave this way. Before complicating things by adding new columns and tables, consider if you can simplify the solution and still meet the requirements. One case being evaluated involves changing how certain UsageData is calculated to remove a join query in https://gitlab.com/gitlab-org/gitlab/-/issues/336170. This is a good candidate to evaluate, because UsageData is not critical to users and it may be possible to get a similarly useful metric with a simpler approach. Alternatively we may find that nobody is using these metrics, so we can remove them.

Use `preload` instead of `includes`

The includes and preload methods in Rails are both ways to avoid an N+1 query. The includes method in Rails uses a heuristic approach to determine if it needs to join to the table, or if it can load all of the records in a separate query. This method assumes it needs to join if it thinks you need to query the columns from the other table, but sometimes this method gets it wrong and executes a join even when not needed. In this case using preload to explicitly load the data in a separate query allows you to avoid the join, while still avoiding the N+1 query.

You can see a real example of this solution being used in https://gitlab.com/gitlab-org/gitlab/-/merge_requests/67655.

De-normalize some foreign key to the table

De-normalization refers to adding redundant precomputed (duplicated) data to a table to simplify certain queries or to improve performance. In this case, it can be useful when you are doing a join that involves three tables, where you are joining through some intermediate table.

Generally when modeling a database schema, a "normalized" structure is preferred because of the following reasons:

Duplicate data uses extra storage.
Duplicate data needs to be kept in sync.

Sometimes normalized data is less performant so de-normalization has been a common technique GitLab has used to improve the performance of database queries for a while. The above problems are mitigated when the following conditions are met:

There isn't much data (for example, it's just an integer column).
The data does not update often (for example, the project_id column is almost never updated for most tables).

One example we found was the security_scans table. This table has a foreign key security_scans.build_id which allows you to join to the build. Therefore you could join to the project like so:

select projects.* from security_scans
inner join ci_builds on security_scans.build_id = ci_builds.id
inner join projects on ci_builds.project_id = projects.id

The problem with this query is that ci_builds is in a different database from the other two tables.

The solution in this case is to add the project_id column to security_scans. This doesn't use much extra storage, and due to the way these features work, it's never updated (a build never moves projects).

This simplified the query to:

select projects.* from security_scans
inner join projects on security_scans.project_id = projects.id

This also improves performance because you don't need to join through an extra table.

You can see this approach implemented in https://gitlab.com/gitlab-org/gitlab/-/merge_requests/66963 . This MR also de-normalizes pipeline_id to fix a similar query.

De-normalize into an extra table

Sometimes the previous de-normalization (adding an extra column) doesn't work for your specific case. This may be due to the fact that your data is not 1:1, or because the table you're adding to is already too wide (for example, the projects table shouldn't have more columns added).

In this case you may decide to just store the extra data in a separate table.

One example where this approach is being used was to implement the Project.with_code_coverage scope. This scope was essentially used to narrow down a list of projects to only those that have at one point in time used code coverage features. This query (simplified) was:

select projects.* from projects
inner join ci_daily_build_group_report_results on ci_daily_build_group_report_results.project_id = projects.id
where ((data->'coverage') is not null)
and ci_daily_build_group_report_results.default_branch = true
group by projects.id

This work is still in progress but the current plan is to introduce a new table called projects_with_ci_feature_usage which has 2 columns project_id and ci_feature. This table would be written to the first time a project creates a ci_daily_build_group_report_results for code coverage. Therefore the new query would be:

select projects.* from projects
inner join projects_with_ci_feature_usage on projects_with_ci_feature_usage.project_id = projects.id
where projects_with_ci_feature_usage.ci_feature = 'code_coverage'

The above example uses as a text column for simplicity but we should probably use an enum to save space.

The downside of this new design is that this may need to be updated (removed if the ci_daily_build_group_report_results is deleted). Depending on your domain, however, this may not be necessary because deletes are edge cases or impossible, or because the user impact of seeing the project on the list page may not be problematic. It's also possible to implement the logic to delete these rows if or whenever necessary in your domain.

Finally, this de-normalization and new query also improves performance because it does less joins and needs less filtering.

Remove a redundant join

Sometimes there are cases where a query is doing excess (or redundant) joins.

A common example occurs where a query is joining from A to C, via some table with both foreign keys, B. When you only care about counting how many rows there are in C and if there are foreign keys and NOT NULL constraints on the foreign keys in B, then it might be enough to count those rows. For example, in MR 71811, it was previously doing project.runners.count, which would produce a query like:

select count(*) from projects
inner join ci_runner_projects on ci_runner_projects.project_id = projects.id
where ci_runner_projects.runner_id IN (1, 2, 3)

This was changed to avoid the cross-join by changing the code to project.runner_projects.count. It produces the same response with the following query:

select count(*) from ci_runner_projects
where ci_runner_projects.runner_id IN (1, 2, 3)

Another common redundant join is joining all the way to another table, then filtering by primary key when you could have instead filtered on a foreign key. See an example in MR 71614. The previous code was joins(scan: :build).where(ci_builds: { id: build_ids }), which generated a query like:

select ...
inner join security_scans
inner join ci_builds on security_scans.build_id = ci_builds.id
where ci_builds.id IN (1, 2, 3)

However, as security_scans already has a foreign key build_id, the code can be changed to joins(:scan).where(security_scans: { build_id: build_ids }), which produces the same response with the following query:

select ...
inner join security_scans
where security_scans.build_id IN (1, 2, 3)

Both of these examples of removing redundant joins remove the cross-joins, but they have the added benefit of producing simpler and faster queries.

Use `disable_joins` for `has_one` or `has_many` `through:` relations

Sometimes a join query is caused by using has_one ... through: or has_many ... through: across tables that span the different databases. These joins sometimes can be solved by adding disable_joins:true. This is a Rails feature which we backported. We also extended the feature to allow a lambda syntax for enabling disable_joins with a feature flag. If you use this feature we encourage using a feature flag as it mitigates risk if there is some serious performance regression.

You can see an example where this was used in https://gitlab.com/gitlab-org/gitlab/-/merge_requests/66709/diffs.

With any change to DB queries it is important to analyze and compare the SQL before and after the change. disable_joins can introduce very poorly performing code depending on the actual logic of the has_many or has_one relationship. The key thing to look for is whether any of the intermediate result sets used to construct the final result set have an unbounded amount of data loaded. The best way to tell is by looking at the SQL generated and confirming that each one is limited in some way. You can tell by either a LIMIT 1 clause or by WHERE clause that is limiting based on a unique column. Any unbounded intermediate dataset could lead to loading too many IDs into memory.

An example where you may see very poor performance is the following hypothetical code:

class Project
  has_many :pipelines
  has_many :builds, through: :pipelines
end

class Pipeline
  has_many :builds
end

class Build
  belongs_to :pipeline
end

def some_action
  @builds = Project.find(5).builds.order(created_at: :desc).limit(10)
end

In the above case some_action will generate a query like:

select * from builds
inner join pipelines on builds.pipeline_id = pipelines.id
where pipelines.project_id = 5
order by builds.created_at desc
limit 10

However, if you changed the relation to be:

class Project
  has_many :pipelines
  has_many :builds, through: :pipelines, disable_joins: true
end

Then you would get the following 2 queries:

select id from pipelines where project_id = 5;

select * from builds where pipeline_id in (...)
order by created_at desc
limit 10;

Because the first query does not limit by any unique column or have a LIMIT clause, it can load an unlimited number of pipeline IDs into memory, which are then sent in the following query. This can lead to very poor performance in the Rails application and the database. In cases like this, you might need to re-write the query or look at other patterns described above for removing cross-joins.

How to validate you have correctly removed a cross-join

Using RSpec tests, you can validate all SQL queries within a code block to ensure that none of them are joining across the two databases. This is a useful tool to confirm you have correctly fixed an existing cross-join.

At some point in the future we will have fixed all cross-joins and this tool will run by default in all tests. For now, the tool needs to be explicitly enabled for your test.

You can use this method like so:

it 'does not join across databases' do
  with_cross_joins_prevented do
    ::Ci::Build.joins(:project).to_a
  end
end

This will raise an exception if the query joins across the two databases. The previous example is fixed by removing the join, like so:

it 'does not join across databases' do
  with_cross_joins_prevented do
    ::Ci::Build.preload(:project).to_a
  end
end

You can see a real example of using this method for fixing a cross-join in https://gitlab.com/gitlab-org/gitlab/-/merge_requests/67655.

Allowlist for existing cross-joins

A cross-join across databases can be explicitly allowed by wrapping the code in the ::Gitlab::Database.allow_cross_joins_across_databases helper method. Alternative way is to mark a given relation as relation.allow_cross_joins_across_databases.

This method should only be used:

For existing code.
If the code is required to help migrate away from a cross-join. For example, in a migration that backfills data for future use to remove a cross-join.

The allow_cross_joins_across_databases helper method can be used as follows:

# Scope the block executing a object from database
::Gitlab::Database.allow_cross_joins_across_databases(url: 'https://gitlab.com/gitlab-org/gitlab/-/issues/336590') do
  subject.perform(1, 4)
end

# Mark a relation as allowed to cross-join databases
def find_actual_head_pipeline
  all_pipelines
    .allow_cross_joins_across_databases(url: 'https://gitlab.com/gitlab-org/gitlab/-/issues/336891')
    .for_sha_or_source_sha(diff_head_sha)
    .first
end

The url parameter should point to an issue with a milestone for when we intend to fix the cross-join. If the cross-join is being used in a migration, we do not need to fix the code. See https://gitlab.com/gitlab-org/gitlab/-/issues/340017 for more details.

Removing cross-database transactions

When dealing with multiple databases, it's important to pay close attention to data modification that affects more than one database. Introduced GitLab 14.4, an automated check prevents cross-database modifications.

When at least two different databases are modified during a transaction initiated on any database server, the application triggers a cross-database modification error (only in test environment).

Example:

# Open transaction on Main DB
ApplicationRecord.transaction do
  ci_build.update!(updated_at: Time.current) # UPDATE on CI DB
  ci_build.project.update!(updated_at: Time.current) # UPDATE on Main DB
end
# raises error: Cross-database data modification of 'main, ci' were detected within
# a transaction modifying the 'ci_build, projects' tables

The code example above updates the timestamp for two records within a transaction. With the ongoing work on the CI database decomposition, we cannot ensure the schematics of a database transaction. If the second update query fails, the first update query will not be rolled back because the ci_build record is located on a different database server. For more information, look at the transaction guidelines page.

Fixing cross-database errors

Removing the transaction block

Without an open transaction, the cross-database modification check cannot raise an error. By making this change, we sacrifice consistency. In case of an application failure after the first UPDATE query, the second UPDATE query will never execute.

The same code without the transaction block:

ci_build.update!(updated_at: Time.current) # CI DB
ci_build.project.update!(updated_at: Time.current) # Main DB

Async processing

If we need more guarantee that an operation finishes the work consistently we can execute it within a background job. A background job is scheduled asynchronously and retried several times in case of an error. There is still a very small chance of introducing inconsistency.

Example:

current_time = Time.current

MyAsyncConsistencyJob.perform_async(cu_build.id)

ci_build.update!(updated_at: current_time)
ci_build.project.update!(updated_at: current_time)

The MyAsyncConsistencyJob would also attempt to update the timestamp if they differ.

Aiming for perfect consistency

At this point, we don't have the tooling (we might not even need it) to ensure similar consistency characteristics as we had with one database. If you think that the code you're working on requires these properties, then you can disable the cross-database modification check by wrapping to offending database queries with a block and create a follow-up issue mentioning the sharding group (gitlab-org/sharding-group).

Gitlab::Database.allow_cross_joins_across_databases(url: 'gitlab issue URL') do
  ApplicationRecord.transaction do
    ci_build.update!(updated_at: Time.current) # UPDATE on CI DB
    ci_build.project.update!(updated_at: Time.current) # UPDATE on Main DB
  end
end

Don't hesitate to reach out to the sharding group for advice.

Avoid `dependent: :nullify` and `dependent: :destroy` across databases

There may be cases where we want to use dependent: :nullify or dependent: :destroy across databases. This is technically possible, but it's problematic because these hooks run in the context of an outer transaction from the call to #destroy, which creates a cross-database transaction and we are trying to avoid that. Cross-database transactions caused this way could lead to confusing outcomes when we switch to decomposed, because now you have some queries happening outside the transaction and they may be partially applied while the outer transaction fails, which could lead to surprising bugs.

If you need to do some cleanup after a destroy you will need to choose from some of the options above. If all you need to do is cleanup the child records themselves from PostgreSQL then you could consider using "loose foreign keys".

`config/database.yml`

GitLab is adding support to run multiple databases, for example to separate tables for the continuous integration features from the main database. In order to prepare for this change, we validate the structure of the configuration in database.yml to ensure that only known databases are used.

Previously, the config/database.yml looked like this:

production:
  adapter: postgresql
  encoding: unicode
  database: gitlabhq_production
  ...

With the support for many databases this syntax is deprecated and will be removed in 15.0.

The new config/database.yml needs to include a database name to define a database configuration. Only main: and ci: database names are supported. The main: database must always be a first entry in a hash. This change applies to decomposed and non-decomposed change. If an invalid or deprecated syntax is used the error or warning is printed during application start.

# Non-decomposed database
production:
  main:
    adapter: postgresql
    encoding: unicode
    database: gitlabhq_production
    ...

# Decomposed database
production:
  main:
    adapter: postgresql
    encoding: unicode
    database: gitlabhq_production
    ...
  ci:
    adapter: postgresql
    encoding: unicode
    database: gitlabhq_production_ci
    ...

Foreign keys that cross databases

There are many places where we use foreign keys that reference across the two databases. This is not possible to do with two separate PostgreSQL databases, so we need to replicate the behavior we get from PostgreSQL in a performant way. We can't, and shouldn't, try to replicate the data guarantees given by PostgreSQL which prevent creating invalid references, but we still need a way to replace cascading deletes so we don't end up with orphaned data or records that point to nowhere, which might lead to bugs. As such we created "loose foreign keys" which is an asynchronous process of cleaning up orphaned records.

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