PostgreSQL

This page contains information about PostgreSQL the GitLab Support team uses when troubleshooting. GitLab makes this information public, so that anyone can make use of the Support team’s collected knowledge.

If you’re on a paid tier and aren’t sure how to use these commands, contact Support for assistance with any issues you’re having.

Start a database console

sudo gitlab-psql

sudo gitlab-rails dbconsole --database main

docker exec -it <container-id> gitlab-psql

sudo -u git -H psql -d gitlabhq_production

To exit the console, type: quit.

Other GitLab PostgreSQL documentation

This section is for links to information elsewhere in the GitLab documentation.

Procedures

• Database procedures for Linux package installations including:

  • SSL: enabling, disabling, and verifying.
  • Enabling Write Ahead Log (WAL) archiving.
  • Using an external (non-Omnibus) PostgreSQL installation; and backing it up.
  • Listening on TCP/IP as well as or instead of sockets.
  • Storing data in another location.
  • Destructively reseeding the GitLab database.
  • Guidance around updating packaged PostgreSQL, including how to stop it from happening automatically.

• Information about external PostgreSQL.

• Running Geo with external PostgreSQL.

• Upgrades when running PostgreSQL configured for HA.

• Consuming PostgreSQL from within CI runners.

• Managing PostgreSQL versions on Linux package installations from the Linux package development documentation.

• PostgreSQL scaling

  • Including troubleshooting gitlab-ctl patroni check-leader and PgBouncer errors.

• Developer database documentation, some of which is absolutely not for production use. Including:

  • Understanding EXPLAIN plans.

Support topics

Database deadlocks

References:

• Deadlocks can occur if an instance is flooded with pushes. Provided for context about how GitLab code can have this sort of unanticipated effect in unusual situations.

ERROR: deadlock detected

Three applicable timeouts are identified in the issue #30528; our recommended settings are as follows:

deadlock_timeout = 5s
statement_timeout = 15s
idle_in_transaction_session_timeout = 60s

Quoting from issue #30528:

“If a deadlock is hit, and we resolve it through aborting the transaction after a short period, then the retry mechanisms we already have will make the deadlocked piece of work try again, and it’s unlikely we’ll deadlock multiple times in a row.”

In this case, the guidance we had from development was to drop deadlock_timeout or statement_timeout, but to leave the third setting at 60 seconds. Setting idle_in_transaction protects the database from sessions potentially hanging for days. There’s more discussion in the issue relating to introducing this timeout on GitLab.com.

PostgreSQL defaults:

• statement_timeout = 0 (never)
• idle_in_transaction_session_timeout = 0 (never)

Comments in issue #30528 indicate that these should both be set to at least a number of minutes for all Linux package installations (so they don’t hang indefinitely). However, 15 s for statement_timeout is very short, and is only effective if the underlying infrastructure is very performant.

See current settings with:

sudo gitlab-rails runner "c = ApplicationRecord.connection ; puts c.execute('SHOW statement_timeout').to_a ;
puts c.execute('SHOW deadlock_timeout').to_a ;
puts c.execute('SHOW idle_in_transaction_session_timeout').to_a ;"

It may take a little while to respond.

{"statement_timeout"=>"1min"}
{"deadlock_timeout"=>"0"}
{"idle_in_transaction_session_timeout"=>"1min"}

These settings can be updated in /etc/gitlab/gitlab.rb with:

postgresql['deadlock_timeout'] = '5s'
postgresql['statement_timeout'] = '15s'
postgresql['idle_in_transaction_session_timeout'] = '60s'

Once saved, reconfigure GitLab for the changes to take effect.

Temporarily changing the statement timeout

In some situations, it may be desirable to set a different statement timeout without having to reconfigure GitLab, which in this case would restart Puma and Sidekiq.

For example, a backup may fail with the following errors in the output of the backup command because the statement timeout was too short:

pg_dump: error: Error message from server: server closed the connection unexpectedly

You may also see errors in the PostgreSQL logs:

canceling statement due to statement timeout

To temporarily change the statement timeout:

1. Open /var/opt/gitlab/gitlab-rails/etc/database.yml in an editor

2. Set the value of statement_timeout to 0, which sets an unlimited statement timeout.

3. Confirm in a new Rails console session that this value is used:

   sudo gitlab-rails runner "ActiveRecord::Base.connection_db_config[:variables]"

4. Perform the action for which you need a different timeout (for example the backup or the Rails command).

5. Revert the edit in /var/opt/gitlab/gitlab-rails/etc/database.yml.

Observe (RE)INDEX progress report

In some situations, you might want to observe the progress of a CREATE INDEX or REINDEX operation. For example, you can do this to confirm whether the CREATE INDEX or REINDEX operation is active, or to check which phase the operation is in.

Prerequisites:

• You must use PostgreSQL version 12 or later.

To observe a CREATE INDEX or REINDEX operation:

• Use the built-in pg_stat_progress_create_index view.

For example, from a database console session, run the following command:

SELECT * FROM  pg_stat_progress_create_index \watch 0.2

To learn more about producing human-friendly output and writing data to log files, see this snippet.

Troubleshooting

Database connection is refused

If you encounter the following errors, check if max_connections is high enough to ensure stable connections.

connection to server at "xxx.xxx.xxx.xxx", port 5432 failed: Connection refused
      Is the server running on that host and accepting TCP/IP connections?

psql: error: connection to server on socket "/var/opt/gitlab/postgresql/.s.PGSQL.5432" failed:
FATAL:  sorry, too many clients already

To adjust max_connections, see configuring multiple database connections.

Database is not accepting commands to avoid wraparound data loss

This error likely means that autovacuum is failing to complete its run:

ERROR:  database is not accepting commands to avoid wraparound data loss in database "gitlabhq_production"

Or

 ERROR:  failed to re-find parent key in index "XXX" for deletion target page XXX

To resolve the error, run VACUUM manually:

1. Stop GitLab with the command gitlab-ctl stop.

2. Place the database in single-user mode with the command:

   /opt/gitlab/embedded/bin/postgres --single -D /var/opt/gitlab/postgresql/data gitlabhq_production

3. In the backend> prompt, run VACUUM;. This command can take several minutes to complete.

4. Wait for the command to complete, then press Control + D to exit.

5. Start GitLab with the command gitlab-ctl start.

GitLab database requirements

See database requirements and review and install the required extension list.

Serialization errors in the production/sidekiq log

If you receive errors like this example in your production/sidekiq log, read about setting default_transaction_isolation into read committed to fix the problem:

ActiveRecord::StatementInvalid PG::TRSerializationFailure: ERROR:  could not serialize access due to concurrent update

PostgreSQL replication slot errors

If you receive errors like this example, read about how to resolve PostgreSQL HA replication slot errors:

pg_basebackup: could not create temporary replication slot "pg_basebackup_12345": ERROR:  all replication slots are in use
HINT:  Free one or increase max_replication_slots.

Geo replication errors

If you receive errors like this example, read about how to resolve Geo replication errors:

ERROR: replication slots can only be used if max_replication_slots > 0

FATAL: could not start WAL streaming: ERROR: replication slot "geo_secondary_my_domain_com" does not exist

Command exceeded allowed execution time

PANIC: could not write to file 'pg_xlog/xlogtemp.123': No space left on device

Review Geo configuration and common errors

When troubleshooting problems with Geo, you should:

• Review common Geo errors.
• Review your Geo configuration, including:
  • Reconfiguring hosts and ports.
  • Reviewing and fixing the user and password mappings.

Mismatch in pg_dump and psql versions

If you receive errors like this example, read about how to back up and restore a non-packaged PostgreSQL database:

Dumping PostgreSQL database gitlabhq_production ... pg_dump: error: server version: 13.3; pg_dump version: 14.2
pg_dump: error: aborting because of server version mismatch

Extension btree_gist is not allow-listed

Deploying PostgreSQL on an Azure Database for PostgreSQL - Flexible Server may result in this error:

extension "btree_gist" is not allow-listed for "azure_pg_admin" users in Azure Database for PostgreSQL

To resolve this error, allow-list the extension prior to install.