Troubleshooting GitLab backups

When you back up GitLab, you might encounter the following issues.

When the secrets file is lost

If you didn’t back up the secrets file, you must complete several steps to get GitLab working properly again.

The secrets file is responsible for storing the encryption key for the columns that contain required, sensitive information. If the key is lost, GitLab can’t decrypt those columns, preventing access to the following items:

In cases like CI/CD variables and runner authentication, you can experience unexpected behaviors, such as:

  • Stuck jobs.
  • 500 errors.

In this case, you must reset all the tokens for CI/CD variables and runner authentication, which is described in more detail in the following sections. After resetting the tokens, you should be able to visit your project and the jobs begin running again.

caution
The steps in this section can potentially lead to data loss on the above listed items. Consider opening a Support Request if you’re a Premium or Ultimate customer.

Verify that all values can be decrypted

You can determine if your database contains values that can’t be decrypted by using a Rake task.

Take a backup

You must directly modify GitLab data to work around your lost secrets file.

caution
Be sure to create a full database backup before attempting any changes.

Disable user two-factor authentication (2FA)

Users with 2FA enabled can’t sign in to GitLab. In that case, you must disable 2FA for everyone, after which users must reactivate 2FA.

Reset CI/CD variables

  1. Enter the database console:

    For the Linux package (Omnibus): 

    sudo gitlab-rails dbconsole --database main

    For self-compiled installations: 

    sudo -u git -H bundle exec rails dbconsole -e production --database main

  2. Examine the ci_group_variables and ci_variables tables: 

    SELECT * FROM public."ci_group_variables";
SELECT * FROM public."ci_variables";

    These are the variables that you need to delete.

  3. Delete all variables: 

    DELETE FROM ci_group_variables;
DELETE FROM ci_variables;

  4. If you know the specific group or project from which you wish to delete variables, you can include a WHERE statement to specify that in your DELETE: 

    DELETE FROM ci_group_variables WHERE group_id = <GROUPID>;
DELETE FROM ci_variables WHERE project_id = <PROJECTID>;

You may need to reconfigure or restart GitLab for the changes to take effect.

Reset runner registration tokens

  1. Enter the database console:

    For the Linux package (Omnibus): 

    sudo gitlab-rails dbconsole --database main

    For self-compiled installations: 

    sudo -u git -H bundle exec rails dbconsole -e production --database main

  2. Clear all tokens for projects, groups, and the entire instance:

    caution
    The final UPDATE operation stops the runners from being able to pick up new jobs. You must register new runners.
    -- Clear project tokens
UPDATE projects SET runners_token = null, runners_token_encrypted = null;
-- Clear group tokens
UPDATE namespaces SET runners_token = null, runners_token_encrypted = null;
-- Clear instance tokens
UPDATE application_settings SET runners_registration_token_encrypted = null;
-- Clear key used for JWT authentication
-- This may break the $CI_JWT_TOKEN job variable:
-- https://gitlab.com/gitlab-org/gitlab/-/issues/325965
UPDATE application_settings SET encrypted_ci_jwt_signing_key = null;
-- Clear runner tokens
UPDATE ci_runners SET token = null, token_encrypted = null;

Reset pending pipeline jobs

  1. Enter the database console:

    For the Linux package (Omnibus): 

    sudo gitlab-rails dbconsole --database main

    For self-compiled installations: 

    sudo -u git -H bundle exec rails dbconsole -e production --database main

  2. Clear all the tokens for pending jobs:

    For GitLab 15.3 and earlier: 

    -- Clear build tokens
UPDATE ci_builds SET token = null, token_encrypted = null;

    For GitLab 15.4 and later: 

    -- Clear build tokens
UPDATE ci_builds SET token_encrypted = null;

A similar strategy can be employed for the remaining features. By removing the data that can’t be decrypted, GitLab can be returned to operation, and the lost data can be manually replaced.

Fix integrations and webhooks

If you’ve lost your secrets, the integrations settings and webhooks settings pages might display 500 error messages. Lost secrets might also produce 500 errors when you try to access a repository in a project with a previously configured integration or webhook.

The fix is to truncate the affected tables (those containing encrypted columns). This deletes all your configured integrations, webhooks, and related metadata. You should verify that the secrets are the root cause before deleting any data.

  1. Enter the database console:

    For the Linux package (Omnibus): 

    sudo gitlab-rails dbconsole --database main

    For self-compiled installations: 

    sudo -u git -H bundle exec rails dbconsole -e production --database main

  2. Truncate the following tables: 

    -- truncate web_hooks table
TRUNCATE integrations, chat_names, issue_tracker_data, jira_tracker_data, slack_integrations, web_hooks, zentao_tracker_data, web_hook_logs CASCADE;

Container registry is not restored

If you restore a backup from an environment that uses the container registry to a newly installed environment where the container registry is not enabled, the container registry is not restored.

To also restore the container registry, you need to enable it in the new environment before you restore the backup.

Container registry push failures after restoring from a backup

If you use the container registry, pushes to the registry may fail after restoring your backup on a Linux package (Omnibus) instance after restoring the registry data.

These failures mention permission issues in the registry logs, similar to: 

level=error
msg="response completed with error"
err.code=unknown
err.detail="filesystem: mkdir /var/opt/gitlab/gitlab-rails/shared/registry/docker/registry/v2/repositories/...: permission denied"
err.message="unknown error"

This issue is caused by the restore running as the unprivileged user git, which is unable to assign the correct ownership to the registry files during the restore process (issue #62759).

To get your registry working again: 

sudo chown -R registry:registry /var/opt/gitlab/gitlab-rails/shared/registry/docker

If you changed the default file system location for the registry, run chown against your custom location, instead of /var/opt/gitlab/gitlab-rails/shared/registry/docker.

Backup fails to complete with Gzip error

When running the backup, you may receive a Gzip error message: 

sudo /opt/gitlab/bin/gitlab-backup create
...
Dumping ...
...
gzip: stdout: Input/output error

Backup failed

If this happens, examine the following:

  • Confirm there is sufficient disk space for the Gzip operation. It’s not uncommon for backups that use the default strategy to require half the instance size in free disk space during backup creation.
  • If NFS is being used, check if the mount option timeout is set. The default is 600, and changing this to smaller values results in this error.

Backup fails with File name too long error

During backup, you can get the File name too long error (issue #354984). For example: 

Problem: <class 'OSError: [Errno 36] File name too long:

This problem stops the backup script from completing. To fix this problem, you must truncate the filenames causing the problem. A maximum of 246 characters, including the file extension, is permitted.

caution
The steps in this section can potentially lead to data loss. All steps must be followed strictly in the order given. Consider opening a Support Request if you’re a Premium or Ultimate customer.

Truncating filenames to resolve the error involves:

  • Cleaning up remote uploaded files that aren’t tracked in the database.
  • Truncating the filenames in the database.
  • Rerunning the backup task.

Clean up remote uploaded files

A known issue caused object store uploads to remain after a parent resource was deleted. This issue was resolved.

To fix these files, you must clean up all remote uploaded files that are in the storage but not tracked in the uploads database table.

  1. List all the object store upload files that can be moved to a lost and found directory if they don’t exist in the GitLab database: 

    bundle exec rake gitlab:cleanup:remote_upload_files RAILS_ENV=production

  2. If you are sure you want to delete these files and remove all non-referenced uploaded files, run:

    caution
    The following action is irreversible.
    bundle exec rake gitlab:cleanup:remote_upload_files RAILS_ENV=production DRY_RUN=false

Truncate the filenames referenced by the database

You must truncate the files referenced by the database that are causing the problem. The filenames referenced by the database are stored:

  • In the uploads table.
  • In the references found. Any reference found from other database tables and columns.
  • On the file system.

Truncate the filenames in the uploads table:

  1. Enter the database console:

    For the Linux package (Omnibus): 

    sudo gitlab-rails dbconsole --database main

    For self-compiled installations: 

    sudo -u git -H bundle exec rails dbconsole -e production --database main

  2. Search the uploads table for filenames longer than 246 characters:

    The following query selects the uploads records with filenames longer than 246 characters in batches of 0 to 10000. This improves the performance on large GitLab instances with tables having thousand of records. 

       CREATE TEMP TABLE uploads_with_long_filenames AS
   SELECT ROW_NUMBER() OVER(ORDER BY id) row_id, id, path
   FROM uploads AS u
   WHERE LENGTH((regexp_match(u.path, '[^\\/:*?"<>|\r\n]+$'))[1]) > 246;

   CREATE INDEX ON uploads_with_long_filenames(row_id);

   SELECT
      u.id,
      u.path,
      -- Current filename
      (regexp_match(u.path, '[^\\/:*?"<>|\r\n]+$'))[1] AS current_filename,
      -- New filename
      CONCAT(
         LEFT(SPLIT_PART((regexp_match(u.path, '[^\\/:*?"<>|\r\n]+$'))[1], '.', 1), 242),
         COALESCE(SUBSTRING((regexp_match(u.path, '[^\\/:*?"<>|\r\n]+$'))[1] FROM '\.(?:.(?!\.))+$'))
      ) AS new_filename,
      -- New path
      CONCAT(
         COALESCE((regexp_match(u.path, '(.*\/).*'))[1], ''),
         CONCAT(
            LEFT(SPLIT_PART((regexp_match(u.path, '[^\\/:*?"<>|\r\n]+$'))[1], '.', 1), 242),
            COALESCE(SUBSTRING((regexp_match(u.path, '[^\\/:*?"<>|\r\n]+$'))[1] FROM '\.(?:.(?!\.))+$'))
         )
      ) AS new_path
   FROM uploads_with_long_filenames AS u
   WHERE u.row_id > 0 AND u.row_id <= 10000;

    Output example: 

       -[ RECORD 1 ]----+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
   id               | 34
   path             | public/@hashed/loremipsumdolorsitametconsecteturadipiscingelitseddoeiusmodtemporincididuntutlaboreetdoloremagnaaliquaauctorelitsedvulputatemisitloremipsumdolorsitametconsecteturadipiscingelitseddoeiusmodtemporincididuntutlaboreetdoloremagnaaliquaauctorelitsedvulputatemisit.txt
   current_filename | loremipsumdolorsitametconsecteturadipiscingelitseddoeiusmodtemporincididuntutlaboreetdoloremagnaaliquaauctorelitsedvulputatemisitloremipsumdolorsitametconsecteturadipiscingelitseddoeiusmodtemporincididuntutlaboreetdoloremagnaaliquaauctorelitsedvulputatemisit.txt
   new_filename     | loremipsumdolorsitametconsecteturadipiscingelitseddoeiusmodtemporincididuntutlaboreetdoloremagnaaliquaauctorelitsedvulputatemisitloremipsumdolorsitametconsecteturadipiscingelitseddoeiusmodtemporincididuntutlaboreetdoloremagnaaliquaauctorelits.txt
   new_path         | public/@hashed/loremipsumdolorsitametconsecteturadipiscingelitseddoeiusmodtemporincididuntutlaboreetdoloremagnaaliquaauctorelitsedvulputatemisitloremipsumdolorsitametconsecteturadipiscingelitseddoeiusmodtemporincididuntutlaboreetdoloremagnaaliquaauctorelits.txt

    Where:

    • current_filename: a filename that is more than 246 characters long.
    • new_filename: a filename that has been truncated to 246 characters maximum.
    • new_path: new path considering the new_filename (truncated).

    After you validate the batch results, you must change the batch size (row_id) using the following sequence of numbers (10000 to 20000). Repeat this process until you reach the last record in the uploads table.

  3. Rename the files found in the uploads table from long filenames to new truncated filenames. The following query rolls back the update so you can check the results safely in a transaction wrapper: 

    CREATE TEMP TABLE uploads_with_long_filenames AS
SELECT ROW_NUMBER() OVER(ORDER BY id) row_id, path, id
FROM uploads AS u
WHERE LENGTH((regexp_match(u.path, '[^\\/:*?"<>|\r\n]+$'))[1]) > 246;

CREATE INDEX ON uploads_with_long_filenames(row_id);

BEGIN;
WITH updated_uploads AS (
   UPDATE uploads
   SET
      path =
      CONCAT(
         COALESCE((regexp_match(updatable_uploads.path, '(.*\/).*'))[1], ''),
         CONCAT(
            LEFT(SPLIT_PART((regexp_match(updatable_uploads.path, '[^\\/:*?"<>|\r\n]+$'))[1], '.', 1), 242),
            COALESCE(SUBSTRING((regexp_match(updatable_uploads.path, '[^\\/:*?"<>|\r\n]+$'))[1] FROM '\.(?:.(?!\.))+$'))
         )
      )
   FROM
      uploads_with_long_filenames AS updatable_uploads
   WHERE
      uploads.id = updatable_uploads.id
   AND updatable_uploads.row_id > 0 AND updatable_uploads.row_id  <= 10000
   RETURNING uploads.*
)
SELECT id, path FROM updated_uploads;
ROLLBACK;

    After you validate the batch update results, you must change the batch size (row_id) using the following sequence of numbers (10000 to 20000). Repeat this process until you reach the last record in the uploads table.

  4. Validate that the new filenames from the previous query are the expected ones. If you are sure you want to truncate the records found in the previous step to 246 characters, run the following:

    caution
    The following action is irreversible.
    CREATE TEMP TABLE uploads_with_long_filenames AS
SELECT ROW_NUMBER() OVER(ORDER BY id) row_id, path, id
FROM uploads AS u
WHERE LENGTH((regexp_match(u.path, '[^\\/:*?"<>|\r\n]+$'))[1]) > 246;

CREATE INDEX ON uploads_with_long_filenames(row_id);

UPDATE uploads
SET
path =
   CONCAT(
      COALESCE((regexp_match(updatable_uploads.path, '(.*\/).*'))[1], ''),
      CONCAT(
         LEFT(SPLIT_PART((regexp_match(updatable_uploads.path, '[^\\/:*?"<>|\r\n]+$'))[1], '.', 1), 242),
         COALESCE(SUBSTRING((regexp_match(updatable_uploads.path, '[^\\/:*?"<>|\r\n]+$'))[1] FROM '\.(?:.(?!\.))+$'))
      )
   )
FROM
uploads_with_long_filenames AS updatable_uploads
WHERE
uploads.id = updatable_uploads.id
AND updatable_uploads.row_id > 0 AND updatable_uploads.row_id  <= 10000;

    After you finish the batch update, you must change the batch size (updatable_uploads.row_id) using the following sequence of numbers (10000 to 20000). Repeat this process until you reach the last record in the uploads table.

Truncate the filenames in the references found:

  1. Check if those records are referenced somewhere. One way to do this is to dump the database and search for the parent directory name and filename:

    1. To dump your database, you can use the following command as an example: 

      pg_dump -h /var/opt/gitlab/postgresql/ -d gitlabhq_production > gitlab-dump.tmp

    2. Then you can search for the references using the grep command. Combining the parent directory and the filename can be a good idea. For example: 

      grep public/alongfilenamehere.txt gitlab-dump.tmp

  2. Replace those long filenames using the new filenames obtained from querying the uploads table.

Truncate the filenames on the file system. You must manually rename the files in your file system to the new filenames obtained from querying the uploads table.

Re-run the backup task

After following all the previous steps, re-run the backup task.

Restoring database backup fails when pg_stat_statements was previously enabled

The GitLab backup of the PostgreSQL database includes all SQL statements required to enable extensions that were previously enabled in the database.

The pg_stat_statements extension can only be enabled or disabled by a PostgreSQL user with superuser role. As the restore process uses a database user with limited permissions, it can’t execute the following SQL statements: 

DROP EXTENSION IF EXISTS pg_stat_statements;
CREATE EXTENSION IF NOT EXISTS pg_stat_statements WITH SCHEMA public;

When trying to restore the backup in a PostgreSQL instance that doesn’t have the pg_stats_statements extension, the following error message is displayed: 

ERROR: permission denied to create extension "pg_stat_statements"
HINT: Must be superuser to create this extension.
ERROR: extension "pg_stat_statements" does not exist

When trying to restore in an instance that has the pg_stats_statements extension enabled, the cleaning up step fails with an error message similar to the following: 

rake aborted!
ActiveRecord::StatementInvalid: PG::InsufficientPrivilege: ERROR: must be owner of view pg_stat_statements
/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:42:in `block (4 levels) in <top (required)>'
/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:41:in `each'
/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:41:in `block (3 levels) in <top (required)>'
/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/backup.rake:71:in `block (3 levels) in <top (required)>'
/opt/gitlab/embedded/bin/bundle:23:in `load'
/opt/gitlab/embedded/bin/bundle:23:in `<main>'
Caused by:
PG::InsufficientPrivilege: ERROR: must be owner of view pg_stat_statements
/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:42:in `block (4 levels) in <top (required)>'
/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:41:in `each'
/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:41:in `block (3 levels) in <top (required)>'
/opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/backup.rake:71:in `block (3 levels) in <top (required)>'
/opt/gitlab/embedded/bin/bundle:23:in `load'
/opt/gitlab/embedded/bin/bundle:23:in `<main>'
Tasks: TOP => gitlab:db:drop_tables
(See full trace by running task with --trace)

Prevent the dump file to include pg_stat_statements

To prevent the inclusion of the extension in the PostgreSQL dump file that is part of the backup bundle, enable the extension in any schema except the public schema: 

CREATE SCHEMA adm;
CREATE EXTENSION pg_stat_statements SCHEMA adm;

If the extension was previously enabled in the public schema, move it to a new one: 

CREATE SCHEMA adm;
ALTER EXTENSION pg_stat_statements SET SCHEMA adm;

To query the pg_stat_statements data after changing the schema, prefix the view name with the new schema: 

SELECT * FROM adm.pg_stat_statements limit 0;

To make it compatible with third-party monitoring solutions that expect it to be enabled in the public schema, you need to include it in the search_path: 

set search_path to public,adm;

Fix an existing dump file to remove references to pg_stat_statements

To fix an existing backup file, do the following changes:

  1. Extract from the backup the following file: db/database.sql.gz.
  2. Decompress the file or use an editor that is capable of handling it compressed.

  3. Remove the following lines, or similar ones: 

    CREATE EXTENSION IF NOT EXISTS pg_stat_statements WITH SCHEMA public;

    COMMENT ON EXTENSION pg_stat_statements IS 'track planning and execution statistics of all SQL statements executed';
  4. Save the changes and recompress the file.
  5. Update the backup file with the modified db/database.sql.gz.