GitLab CE upgrade to 18.9 PG::CheckViolation: ERROR

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On an Ubuntu 24.04 server upgrading to GitLab CE 18.9 failed with this error:

rake aborted!
StandardError: An error has occurred, all later migrations canceled:

PG::CheckViolation: ERROR:  check constraint "check_96233d37c0" of relation "pool_repositories" is violated by some row
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:122:in `block in validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/timeout_helpers.rb:31:in `disable_statement_timeout'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:119:in `validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:109:in `add_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:218:in `add_not_null_constraint'


/opt/gitlab/embedded/service/gitlab-rails/db/post_migrate/20260209093954_add_not_null_constraint_to_pool_repositories_organization_id.rb:9:in `up'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:33:in `block in exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/query_analyzer.rb:94:in `within'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:30:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/automatic_lock_writes_on_tables.rb:21:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/require_disable_ddl_transaction_for_multiple_locks.rb:40:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/lock_retry_mixin.rb:46:in `ddl_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/runner_backoff/active_record_mixin.rb:21:in `execute_migration_in_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/pg_backend_pid.rb:14:in `with_advisory_lock'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:226:in `configure_database'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:182:in `configure_pg_databases'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:114:in `block (3 levels) in <top (required)>'


/opt/gitlab/embedded/bin/bundle:25:in `<main>'



Caused by:
ActiveRecord::StatementInvalid: PG::CheckViolation: ERROR:  check constraint "check_96233d37c0" of relation "pool_repositories" is violated by some row
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:122:in `block in validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/timeout_helpers.rb:31:in `disable_statement_timeout'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:119:in `validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:109:in `add_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:218:in `add_not_null_constraint'


/opt/gitlab/embedded/service/gitlab-rails/db/post_migrate/20260209093954_add_not_null_constraint_to_pool_repositories_organization_id.rb:9:in `up'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:33:in `block in exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/query_analyzer.rb:94:in `within'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:30:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/automatic_lock_writes_on_tables.rb:21:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/require_disable_ddl_transaction_for_multiple_locks.rb:40:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/lock_retry_mixin.rb:46:in `ddl_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/runner_backoff/active_record_mixin.rb:21:in `execute_migration_in_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/pg_backend_pid.rb:14:in `with_advisory_lock'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:226:in `configure_database'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:182:in `configure_pg_databases'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:114:in `block (3 levels) in <top (required)>'


/opt/gitlab/embedded/bin/bundle:25:in `<main>'



Caused by:
PG::CheckViolation: ERROR:  check constraint "check_96233d37c0" of relation "pool_repositories" is violated by some row
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:122:in `block in validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/timeout_helpers.rb:31:in `disable_statement_timeout'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:119:in `validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:109:in `add_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:218:in `add_not_null_constraint'


/opt/gitlab/embedded/service/gitlab-rails/db/post_migrate/20260209093954_add_not_null_constraint_to_pool_repositories_organization_id.rb:9:in `up'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:33:in `block in exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/query_analyzer.rb:94:in `within'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:30:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/automatic_lock_writes_on_tables.rb:21:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/require_disable_ddl_transaction_for_multiple_locks.rb:40:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/lock_retry_mixin.rb:46:in `ddl_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/runner_backoff/active_record_mixin.rb:21:in `execute_migration_in_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/pg_backend_pid.rb:14:in `with_advisory_lock'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:226:in `configure_database'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:182:in `configure_pg_databases'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:114:in `block (3 levels) in <top (required)>'


/opt/gitlab/embedded/bin/bundle:25:in `<main>'


Tasks: TOP => db:migrate
(See full trace by running task with --trace)
STDERR: 
---- End output of "bash"  ----
Ran "bash"  returned 1
===
There was an error running gitlab-ctl reconfigure. Please check the output above for more
details.
===

dpkg: error processing package gitlab-ce (--configure):
 installed gitlab-ce package post-installation script subprocess returned error exit status 1
Setting up systemd-hwe-hwdb (255.1.7) ...
Processing triggers for udev (255.4-1ubuntu8.12) ...
Errors were encountered while processing:
 gitlab-ce
needrestart is being skipped since dpkg has failed
E: Sub-process /usr/bin/dpkg returned an error code (1)

Trying to fix this with gitlab-ctl reconfigure resulted in:

rake aborted!
StandardError: An error has occurred, all later migrations canceled:

PG::CheckViolation: ERROR:  check constraint "check_96233d37c0" of relation "pool_repositories" is violated by some row
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:122:in `block in validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/timeout_helpers.rb:31:in `disable_statement_timeout'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:119:in `validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:109:in `add_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:218:in `add_not_null_constraint'


/opt/gitlab/embedded/service/gitlab-rails/db/post_migrate/20260209093954_add_not_null_constraint_to_pool_repositories_organization_id.rb:9:in `up'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:33:in `block in exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/query_analyzer.rb:94:in `within'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:30:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/automatic_lock_writes_on_tables.rb:21:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/require_disable_ddl_transaction_for_multiple_locks.rb:40:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/lock_retry_mixin.rb:46:in `ddl_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/runner_backoff/active_record_mixin.rb:21:in `execute_migration_in_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/pg_backend_pid.rb:14:in `with_advisory_lock'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:226:in `configure_database'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:182:in `configure_pg_databases'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:114:in `block (3 levels) in <top (required)>'


/opt/gitlab/embedded/bin/bundle:25:in `<main>'



Caused by:
ActiveRecord::StatementInvalid: PG::CheckViolation: ERROR:  check constraint "check_96233d37c0" of relation "pool_repositories" is violated by some row
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:122:in `block in validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/timeout_helpers.rb:31:in `disable_statement_timeout'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:119:in `validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:109:in `add_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:218:in `add_not_null_constraint'


/opt/gitlab/embedded/service/gitlab-rails/db/post_migrate/20260209093954_add_not_null_constraint_to_pool_repositories_organization_id.rb:9:in `up'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:33:in `block in exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/query_analyzer.rb:94:in `within'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:30:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/automatic_lock_writes_on_tables.rb:21:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/require_disable_ddl_transaction_for_multiple_locks.rb:40:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/lock_retry_mixin.rb:46:in `ddl_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/runner_backoff/active_record_mixin.rb:21:in `execute_migration_in_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/pg_backend_pid.rb:14:in `with_advisory_lock'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:226:in `configure_database'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:182:in `configure_pg_databases'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:114:in `block (3 levels) in <top (required)>'


/opt/gitlab/embedded/bin/bundle:25:in `<main>'



Caused by:
PG::CheckViolation: ERROR:  check constraint "check_96233d37c0" of relation "pool_repositories" is violated by some row
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:122:in `block in validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/timeout_helpers.rb:31:in `disable_statement_timeout'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:119:in `validate_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:109:in `add_check_constraint'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/constraints_helpers.rb:218:in `add_not_null_constraint'


/opt/gitlab/embedded/service/gitlab-rails/db/post_migrate/20260209093954_add_not_null_constraint_to_pool_repositories_organization_id.rb:9:in `up'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:33:in `block in exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/query_analyzer.rb:94:in `within'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/restrict_gitlab_schema.rb:30:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/automatic_lock_writes_on_tables.rb:21:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migration_helpers/require_disable_ddl_transaction_for_multiple_locks.rb:40:in `exec_migration'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/lock_retry_mixin.rb:46:in `ddl_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/runner_backoff/active_record_mixin.rb:21:in `execute_migration_in_transaction'


/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/database/migrations/pg_backend_pid.rb:14:in `with_advisory_lock'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:226:in `configure_database'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:182:in `configure_pg_databases'


/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:114:in `block (3 levels) in <top (required)>'


/opt/gitlab/embedded/bin/bundle:25:in `<main>'


Tasks: TOP => db:migrate
(See full trace by running task with --trace)
STDERR: 
---- End output of "bash"  ----
Ran "bash"  returned 1

I have found two matches for the string check_96233d37c0 in this project, both merge requests.

Does any have any suggestions regarding how to fix this? Thanks!

Workaround

UPDATE pool_repositories
SET organization_id = (
  SELECT organization_id
  FROM projects
  WHERE projects.id = pool_repositories.source_project_id
)
WHERE organization_id IS NULL;

Edited Mar 30, 2026 by 🤖 GitLab Bot 🤖