debian-mirror-gitlab/doc/administration/geo/replication/troubleshooting.md

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Systems	Geo	To determine the technical writer assigned to the Stage/Group associated with this page, see https://about.gitlab.com/handbook/engineering/ux/technical-writing/#assignments

Troubleshooting Geo (PREMIUM SELF)

Setting up Geo requires careful attention to details, and sometimes it's easy to miss a step.

Here is a list of steps you should take to attempt to fix problem:

1. Perform basic troubleshooting.
2. Fix any replication errors.
3. Fix any common errors.

Basic troubleshooting

Before attempting more advanced troubleshooting:

• Check the health of the secondary node.
• Check if PostgreSQL replication is working.

Check the health of the secondary node

On the primary node:

1. On the top bar, select Menu > Admin.
2. On the left sidebar, select Geo > Nodes.

We perform the following health checks on each secondary node to help identify if something is wrong:

• Is the node running?
• Is the node's secondary database configured for streaming replication?
• Is the node's secondary tracking database configured?
• Is the node's secondary tracking database connected?
• Is the node's secondary tracking database up-to-date?

For information about how to resolve common error messages reported from the user interface, see Fixing Common Errors.

If the user interface is not working, or you are unable to sign in, you can run the Geo health check manually to get this information and a few more details.

Health check Rake task

This Rake task can be run on an app node in the primary or secondary Geo nodes:

sudo gitlab-rake gitlab:geo:check

Example output:

Checking Geo ...

GitLab Geo is available ... yes
GitLab Geo is enabled ... yes
This machine's Geo node name matches a database record ... yes, found a secondary node named "Shanghai"
GitLab Geo secondary database is correctly configured ... yes
Database replication enabled? ... yes
Database replication working? ... yes
GitLab Geo HTTP(S) connectivity ...
* Can connect to the primary node ... yes
HTTP/HTTPS repository cloning is enabled ... yes
Machine clock is synchronized ... yes
Git user has default SSH configuration? ... yes
OpenSSH configured to use AuthorizedKeysCommand ... yes
GitLab configured to disable writing to authorized_keys file ... yes
GitLab configured to store new projects in hashed storage? ... yes
All projects are in hashed storage? ... yes

Checking Geo ... Finished

Sync status Rake task

Current sync information can be found manually by running this Rake task on any node running Rails (Puma, Sidekiq, or Geo Log Cursor) on the Geo secondary site:

sudo gitlab-rake geo:status

The output includes:

• a count of "failed" items if any failures occurred
• the percentage of "succeeded" items, relative to the "total"

Example:

http://secondary.example.com/
-----------------------------------------------------
                        GitLab Version: 14.9.2-ee
                              Geo Role: Secondary
                         Health Status: Healthy
                          Repositories: succeeded 12345 / total 12345 (100%)
                 Verified Repositories: succeeded 12345 / total 12345 (100%)
                                 Wikis: succeeded 6789 / total 6789 (100%)
                        Verified Wikis: succeeded 6789 / total 6789 (100%)
                           Attachments: succeeded 4 / total 4 (100%)
                      CI job artifacts: succeeded 0 / total 0 (0%)
                   Design repositories: succeeded 1 / total 1 (100%)
                           LFS Objects: failed 1 / succeeded 2 / total 3 (67%)
                   Merge Request Diffs: succeeded 0 / total 0 (0%)
                         Package Files: failed 1 / succeeded 2 / total 3 (67%)
              Terraform State Versions: failed 1 / succeeded 2 / total 3 (67%)
                  Snippet Repositories: failed 1 / succeeded 2 / total 3 (67%)
               Group Wiki Repositories: succeeded 4 / total 4 (100%)
                    Pipeline Artifacts: failed 3 / succeeded 0 / total 3 (0%)
                     Pages Deployments: succeeded 0 / total 0 (0%)
                  Repositories Checked: failed 5 / succeeded 0 / total 5 (0%)
                Package Files Verified: succeeded 0 / total 10 (0%)
     Terraform State Versions Verified: succeeded 0 / total 10 (0%)
         Snippet Repositories Verified: succeeded 99 / total 100 (99%)
           Pipeline Artifacts Verified: succeeded 0 / total 10 (0%)
                         Sync Settings: Full
              Database replication lag: 0 seconds
       Last event ID seen from primary: 12345 (about 2 minutes ago)
     Last event ID processed by cursor: 12345 (about 2 minutes ago)
                Last status report was: 1 minute ago

To find more details about failed items, check the gitlab-rails/geo.log file

Check if PostgreSQL replication is working

To check if PostgreSQL replication is working, check if:

• Sites are pointing to the correct database node.
• Geo can detect the current site correctly.

Are sites pointing to the correct database node?

You should make sure your primary Geo site points to the database node that has write permissions.

Any secondary sites should point only to read-only database nodes.

Can Geo detect the current site correctly?

Geo finds the current Puma or Sidekiq node's Geo site name in /etc/gitlab/gitlab.rb with the following logic:

1. Get the "Geo node name" (there is an issue to rename the settings to "Geo site name"):
   • Omnibus GitLab: Get the gitlab_rails['geo_node_name'] setting.
   • GitLab Helm Charts: Get the global.geo.nodeName setting (see Charts with GitLab Geo).
2. If that is not defined, then get the external_url setting.

This name is used to look up the Geo site with the same Name in the Geo Sites dashboard.

To check if the current machine has a site name that matches a site in the database, run the check task:

sudo gitlab-rake gitlab:geo:check

It displays the current machine's site name and whether the matching database record is a primary or secondary site.

This machine's Geo node name matches a database record ... yes, found a secondary node named "Shanghai"

This machine's Geo node name matches a database record ... no
  Try fixing it:
  You could add or update a Geo node database record, setting the name to "https://example.com/".
  Or you could set this machine's Geo node name to match the name of an existing database record: "London", "Shanghai"
  For more information see:
  doc/administration/geo/replication/troubleshooting.md#can-geo-detect-the-current-node-correctly

Learn more about recommended site names in the description of the Name field in Geo Admin Area Common Settings.

Message: WARNING: oldest xmin is far in the past and pg_wal size growing

If a replication slot is inactive, the pg_wal logs corresponding to the slot are reserved forever (or until the slot is active again). This causes continuous disk usage growth and the following messages appear repeatedly in the PostgreSQL logs:

WARNING: oldest xmin is far in the past
HINT: Close open transactions soon to avoid wraparound problems.
You might also need to commit or roll back old prepared transactions, or drop stale replication slots.

To fix this:

1. Connect to the primary database.

2. Run SELECT * FROM pg_replication_slots;. Note the slot_name that reports active as f (false).

3. Follow the steps to remove that Geo site.

Fixing errors found when running the Geo check Rake task

When running this Rake task, you may see error messages if the nodes are not properly configured:

sudo gitlab-rake gitlab:geo:check

• Rails did not provide a password when connecting to the database.

  Checking Geo ...
  
  GitLab Geo is available ... Exception: fe_sendauth: no password supplied
  GitLab Geo is enabled ... Exception: fe_sendauth: no password supplied
  ...
  Checking Geo ... Finished
  

  Ensure you have the gitlab_rails['db_password'] set to the plain-text password used when creating the hash for postgresql['sql_user_password'].

• Rails is unable to connect to the database.

  Checking Geo ...
  
  GitLab Geo is available ... Exception: FATAL:  no pg_hba.conf entry for host "1.1.1.1",  user "gitlab", database "gitlabhq_production", SSL on
  FATAL:  no pg_hba.conf entry for host "1.1.1.1", user "gitlab", database "gitlabhq_production", SSL off
  GitLab Geo is enabled ... Exception: FATAL:  no pg_hba.conf entry for host "1.1.1.1", user "gitlab", database "gitlabhq_production", SSL on
  FATAL:  no pg_hba.conf entry for host "1.1.1.1", user "gitlab", database "gitlabhq_production", SSL off
  ...
  Checking Geo ... Finished
  

  Ensure you have the IP address of the rails node included in postgresql['md5_auth_cidr_addresses']. Also, ensure you have included the subnet mask on the IP address: postgresql['md5_auth_cidr_addresses'] = ['1.1.1.1/32'].

• Rails has supplied the incorrect password.

  Checking Geo ...
  GitLab Geo is available ... Exception: FATAL:  password authentication failed for user "gitlab"
  FATAL:  password authentication failed for user "gitlab"
  GitLab Geo is enabled ... Exception: FATAL:  password authentication failed for user "gitlab"
  FATAL:  password authentication failed for user "gitlab"
  ...
  Checking Geo ... Finished
  

  Verify the correct password is set for gitlab_rails['db_password'] that was used when creating the hash in postgresql['sql_user_password'] by running gitlab-ctl pg-password-md5 gitlab and entering the password.

• Check returns not a secondary node.

  Checking Geo ...
  
  GitLab Geo is available ... yes
  GitLab Geo is enabled ... yes
  GitLab Geo secondary database is correctly configured ... not a secondary node
  Database replication enabled? ... not a secondary node
  ...
  Checking Geo ... Finished
  

  Ensure you have added the secondary node in the Admin Area of the primary node. Also ensure you entered the external_url or gitlab_rails['geo_node_name'] when adding the secondary node in the Admin Area of the primary node. In GitLab 12.3 and earlier, edit the secondary node in the Admin Area of the primary node and ensure that there is a trailing / in the Name field.

• Check returns Exception: PG::UndefinedTable: ERROR: relation "geo_nodes" does not exist.

  Checking Geo ...
  
  GitLab Geo is available ... no
    Try fixing it:
    Add a new license that includes the GitLab Geo feature
    For more information see:
    https://about.gitlab.com/features/gitlab-geo/
  GitLab Geo is enabled ... Exception: PG::UndefinedTable: ERROR:  relation "geo_nodes" does not exist
  LINE 8:                WHERE a.attrelid = '"geo_nodes"'::regclass
                                             ^
  :               SELECT a.attname, format_type(a.atttypid, a.atttypmod),
                       pg_get_expr(d.adbin, d.adrelid), a.attnotnull, a.atttypid, a.atttypmod,
                       c.collname, col_description(a.attrelid, a.attnum) AS comment
                  FROM pg_attribute a
                  LEFT JOIN pg_attrdef d ON a.attrelid = d.adrelid AND a.attnum = d.adnum
                  LEFT JOIN pg_type t ON a.atttypid = t.oid
                  LEFT JOIN pg_collation c ON a.attcollation = c.oid AND a.attcollation <> t.typcollation
                 WHERE a.attrelid = '"geo_nodes"'::regclass
                   AND a.attnum > 0 AND NOT a.attisdropped
                 ORDER BY a.attnum
  ...
  Checking Geo ... Finished
  

  When performing a PostgreSQL major version (9 > 10) update this is expected. Follow the initiate-the-replication-process.

Fixing replication errors

The following sections outline troubleshooting steps for fixing replication error messages (indicated by Database replication working? ... no in the geo:check output.

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

This means that the max_replication_slots PostgreSQL variable needs to be set on the primary database. This setting defaults to 1. You may need to increase this value if you have more secondary nodes.

Be sure to restart PostgreSQL for this to take effect. See the PostgreSQL replication setup guide for more details.

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

This occurs when PostgreSQL does not have a replication slot for the secondary node by that name.

You may want to rerun the replication process on the secondary node .

Message: "Command exceeded allowed execution time" when setting up replication?

This may happen while initiating the replication process on the secondary node, and indicates your initial dataset is too large to be replicated in the default timeout (30 minutes).

Re-run gitlab-ctl replicate-geo-database, but include a larger value for --backup-timeout:

sudo gitlab-ctl \
   replicate-geo-database \
   --host=<primary_node_hostname> \
   --slot-name=<secondary_slot_name> \
   --backup-timeout=21600

This gives the initial replication up to six hours to complete, rather than the default 30 minutes. Adjust as required for your installation.

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

Determine if you have any unused replication slots in the primary database. This can cause large amounts of log data to build up in pg_xlog. Removing the unused slots can reduce the amount of space used in the pg_xlog.

1. Start a PostgreSQL console session:

   sudo gitlab-psql
   

   NOTE: Using gitlab-rails dbconsole does not work, because managing replication slots requires superuser permissions.

2. View your replication slots:

   SELECT * FROM pg_replication_slots;
   

Slots where active is f are not active.

• When this slot should be active, because you have a secondary node configured using that slot, sign in to that secondary node and check the PostgreSQL logs to view why the replication is not running.

• If you are no longer using the slot (for example, you no longer have Geo enabled), you can remove it with in the PostgreSQL console session:

  SELECT pg_drop_replication_slot('<name_of_extra_slot>');
  

Message: "ERROR: canceling statement due to conflict with recovery"

This error message occurs infrequently under normal usage, and the system is resilient enough to recover.

However, under certain conditions, some database queries on secondaries may run excessively long, which increases the frequency of this error message. This can lead to a situation where some queries never complete due to being canceled on every replication.

These long-running queries are planned to be removed in the future, but as a workaround, we recommend enabling hot_standby_feedback. This increases the likelihood of bloat on the primary node as it prevents VACUUM from removing recently-dead rows. However, it has been used successfully in production on GitLab.com.

To enable hot_standby_feedback, add the following to /etc/gitlab/gitlab.rb on the secondary node:

postgresql['hot_standby_feedback'] = 'on'

Then reconfigure GitLab:

sudo gitlab-ctl reconfigure

To help us resolve this problem, consider commenting on the issue.

Message: FATAL: could not connect to the primary server: server certificate for "PostgreSQL" does not match host name

This happens because the PostgreSQL certificate that the Omnibus GitLab package automatically creates contains the Common Name PostgreSQL, but the replication is connecting to a different host and GitLab attempts to use the verify-full SSL mode by default.

In order to fix this, you can either:

• Use the --sslmode=verify-ca argument with the replicate-geo-database command.
• For an already replicated database, change sslmode=verify-full to sslmode=verify-ca in /var/opt/gitlab/postgresql/data/gitlab-geo.conf and run gitlab-ctl restart postgresql.
• Configure SSL for PostgreSQL with a custom certificate (including the host name that's used to connect to the database in the CN or SAN) instead of using the automatically generated certificate.

Message: LOG: invalid CIDR mask in address

This happens on wrongly-formatted addresses in postgresql['md5_auth_cidr_addresses'].

2020-03-20_23:59:57.60499 LOG:  invalid CIDR mask in address "***"
2020-03-20_23:59:57.60501 CONTEXT:  line 74 of configuration file "/var/opt/gitlab/postgresql/data/pg_hba.conf"

To fix this, update the IP addresses in /etc/gitlab/gitlab.rb under postgresql['md5_auth_cidr_addresses'] to respect the CIDR format (that is, 1.2.3.4/32).

Message: LOG: invalid IP mask "md5": Name or service not known

This happens when you have added IP addresses without a subnet mask in postgresql['md5_auth_cidr_addresses'].

2020-03-21_00:23:01.97353 LOG:  invalid IP mask "md5": Name or service not known
2020-03-21_00:23:01.97354 CONTEXT:  line 75 of configuration file "/var/opt/gitlab/postgresql/data/pg_hba.conf"

To fix this, add the subnet mask in /etc/gitlab/gitlab.rb under postgresql['md5_auth_cidr_addresses'] to respect the CIDR format (that is, 1.2.3.4/32).

Message: Found data in the gitlabhq_production database! when running gitlab-ctl replicate-geo-database

This happens if data is detected in the projects table. When one or more projects are detected, the operation is aborted to prevent accidental data loss. To bypass this message, pass the --force option to the command.

In GitLab 13.4, a seed project is added when GitLab is first installed. This makes it necessary to pass --force even on a new Geo secondary node. There is an issue to account for seed projects when checking the database.

Message: Synchronization failed - Error syncing repository

WARNING: If large repositories are affected by this problem, their resync may take a long time and cause significant load on your Geo nodes, storage and network systems.

If you see the error message Synchronization failed - Error syncing repository along with fatal: fsck error in packed object, this indicates a consistency check error when syncing the repository.

One example of a consistency error is: error: object f4a87a3be694fbbd6e50a668a31a8513caeaafe3: hasDotgit: contains '.git.

Removing the malformed objects causing consistency errors require rewriting the repository history, which is not always an option. However, it's possible to override the consistency checks instead. To do that, follow the instructions in the Gitaly docs.

You can also get the error message Synchronization failed - Error syncing repository along with the following log messages, this indicates that the expected geo remote is not present in the .git/config file of a repository on the secondary Geo node's file system:

{
  "created": "@1603481145.084348757",
  "description": "Error received from peer unix:/var/opt/gitlab/gitaly/gitaly.socket",
  …
  "grpc_message": "exit status 128",
  "grpc_status": 13
}
{  …
  "grpc.request.fullMethod": "/gitaly.RemoteService/FindRemoteRootRef",
  "grpc.request.glProjectPath": "<namespace>/<project>",
  …
  "level": "error",
  "msg": "fatal: 'geo' does not appear to be a git repository
          fatal: Could not read from remote repository. …",
}

To solve this:

1. Sign in to the secondary Geo node.

2. Back up the .git folder.

3. Optional. Spot-check a few of those IDs whether they indeed correspond to a project with known Geo replication failures. Use fatal: 'geo' as the grep term and the following API call:

   curl --request GET --header "PRIVATE-TOKEN: <your_access_token>" "https://gitlab.example.com/api/v4/projects/<first_failed_geo_sync_ID>"
   

4. Enter the Rails console and run:

   failed_geo_syncs = Geo::ProjectRegistry.failed.pluck(:id)
   failed_geo_syncs.each do |fgs|
     puts Geo::ProjectRegistry.failed.find(fgs).project_id
   end
   

5. Run the following commands to reset each project's Geo-related attributes and execute a new sync:

   failed_geo_syncs.each do |fgs|
     registry = Geo::ProjectRegistry.failed.find(fgs)
     registry.update(resync_repository: true, force_to_redownload_repository: false, repository_retry_count: 0)
     Geo::RepositorySyncService.new(registry.project).execute
   end
   

Very large repositories never successfully synchronize on the secondary node

GitLab places a timeout on all repository clones, including project imports and Geo synchronization operations. If a fresh git clone of a repository on the primary takes more than the default three hours, you may be affected by this.

To increase the timeout:

1. On the secondary node, add the following line to /etc/gitlab/gitlab.rb:

   gitlab_rails['gitlab_shell_git_timeout'] = 14400
   

2. Reconfigure GitLab:

   sudo gitlab-ctl reconfigure
   

This increases the timeout to four hours (14400 seconds). Choose a time long enough to accommodate a full clone of your largest repositories.

New LFS objects are never replicated

If new LFS objects are never replicated to secondary Geo nodes, check the version of GitLab you are running. GitLab versions 11.11.x or 12.0.x are affected by a bug that results in new LFS objects not being replicated to Geo secondary nodes.

To resolve the issue, upgrade to GitLab 12.1 or later.

Failures during backfill

During a backfill, failures are scheduled to be retried at the end of the backfill queue, therefore these failures only clear up after the backfill completes.

Resetting Geo secondary node replication

If you get a secondary node in a broken state and want to reset the replication state, to start again from scratch, there are a few steps that can help you:

1. Stop Sidekiq and the Geo LogCursor.

   It's possible to make Sidekiq stop gracefully, but making it stop getting new jobs and wait until the current jobs to finish processing.

   You need to send a SIGTSTP kill signal for the first phase and them a SIGTERM when all jobs have finished. Otherwise just use the gitlab-ctl stop commands.

   gitlab-ctl status sidekiq
   # run: sidekiq: (pid 10180) <- this is the PID you will use
   kill -TSTP 10180 # change to the correct PID
   
   gitlab-ctl stop sidekiq
   gitlab-ctl stop geo-logcursor
   

   You can watch the Sidekiq logs to know when Sidekiq jobs processing has finished:

   gitlab-ctl tail sidekiq
   

2. Rename repository storage folders and create new ones. If you are not concerned about possible orphaned directories and files, you can skip this step.

   mv /var/opt/gitlab/git-data/repositories /var/opt/gitlab/git-data/repositories.old
   mkdir -p /var/opt/gitlab/git-data/repositories
   chown git:git /var/opt/gitlab/git-data/repositories
   

   NOTE: You may want to remove the /var/opt/gitlab/git-data/repositories.old in the future as soon as you confirmed that you don't need it anymore, to save disk space.

3. Optional. Rename other data folders and create new ones.

   WARNING: You may still have files on the secondary node that have been removed from the primary node, but this removal has not been reflected. If you skip this step, these files are not removed from the Geo node.

   Any uploaded content (like file attachments, avatars, or LFS objects) is stored in a subfolder in one of these paths:

   • /var/opt/gitlab/gitlab-rails/shared
   • /var/opt/gitlab/gitlab-rails/uploads

   To rename all of them:

   gitlab-ctl stop
   
   mv /var/opt/gitlab/gitlab-rails/shared /var/opt/gitlab/gitlab-rails/shared.old
   mkdir -p /var/opt/gitlab/gitlab-rails/shared
   
   mv /var/opt/gitlab/gitlab-rails/uploads /var/opt/gitlab/gitlab-rails/uploads.old
   mkdir -p /var/opt/gitlab/gitlab-rails/uploads
   
   gitlab-ctl start postgresql
   gitlab-ctl start geo-postgresql
   

   Reconfigure to recreate the folders and make sure permissions and ownership are correct:

   gitlab-ctl reconfigure
   

4. Reset the Tracking Database.

   WARNING: If you skipped the optional step 3, be sure both geo-postgresql and postgresql services are running.

   gitlab-rake db:drop:geo DISABLE_DATABASE_ENVIRONMENT_CHECK=1   # on a secondary app node
   gitlab-ctl reconfigure     # on the tracking database node
   gitlab-rake db:migrate:geo # on a secondary app node
   

5. Restart previously stopped services.

   gitlab-ctl start
   

Design repository failures on mirrored projects and project imports

On the top bar, under Menu > Admin > Geo > Nodes, if the Design repositories progress bar shows Synced and Failed greater than 100%, and negative Queued, the instance is likely affected by a bug in GitLab 13.2 and 13.3. It was fixed in GitLab 13.4 and later.

To determine the actual replication status of design repositories in a Rails console:

secondary = Gitlab::Geo.current_node
counts = {}
secondary.designs.select("projects.id").find_each do |p|
  registry = Geo::DesignRegistry.find_by(project_id: p.id)
  state = registry ? "#{registry.state}" : "registry does not exist yet"
  # puts "Design ID##{p.id}: #{state}" # uncomment this for granular information
  counts[state] ||= 0
  counts[state] += 1
end
puts "\nCounts:", counts

Example output:

Design ID#5: started
Design ID#6: synced
Design ID#7: failed
Design ID#8: pending
Design ID#9: synced

Counts:
{"started"=>1, "synced"=>2, "failed"=>1, "pending"=>1}

Example output if there are actually zero design repository replication failures:

Design ID#5: synced
Design ID#6: synced
Design ID#7: synced

Counts:
{"synced"=>3}

If you are promoting a Geo secondary site running on a single server

gitlab-ctl promotion-preflight-checks fails due to the existence of failed rows in the geo_design_registry table. Use the previous snippet to determine the actual replication status of Design repositories.

gitlab-ctl promote-to-primary-node fails since it runs preflight checks. If the previous snippet shows that all designs are synced, you can use the --skip-preflight-checks option or the --force option to move forward with promotion.

If you are promoting a Geo secondary site running on multiple servers

gitlab-ctl promotion-preflight-checks fails due to the existence of failed rows in the geo_design_registry table. Use the previous snippet to determine the actual replication status of Design repositories.

Sync failure message: "Verification failed with: Error during verification: File is not checksummable"

Missing files on the Geo primary site

In GitLab 14.5 and earlier, certain data types which were missing on the Geo primary site were marked as "synced" on Geo secondary sites. This was because from the perspective of Geo secondary sites, the state matched the primary site and nothing more could be done on secondary sites.

Secondaries would regularly try to sync these files again by using the "verification" feature:

• Verification fails since the file doesn't exist.
• The file is marked "sync failed".
• Sync is retried.
• The file is marked "sync succeeded".
• The file is marked "needs verification".
• Repeat until the file is available again on the primary site.

This can be confusing to troubleshoot, since the registry entries are moved through a logical loop by various background jobs. Also, last_sync_failure and verification_failure are empty after "sync succeeded" but before verification is retried.

If you see sync failures repeatedly and alternately increase, while successes decrease and vice versa, this is likely to be caused by missing files on the primary site. You can confirm this by searching geo.log on secondary sites for File is not checksummable affecting the same files over and over.

After confirming this is the problem, the files on the primary site need to be fixed. Some possible causes:

• An NFS share became unmounted.
• A disk died or became corrupted.
• Someone unintentionally deleted a file or directory.
• Bugs in GitLab application:
  • A file was moved when it shouldn't have been moved.
  • A file wasn't moved when it should have been moved.
  • A wrong path was generated in the code.
• A non-atomic backup was restored.
• Services or servers or network infrastructure was interrupted/restarted during use.

The appropriate action sometimes depends on the cause. For example, you can remount an NFS share. Often, a root cause may not be apparent or not useful to discover. If you have regular backups, it may be expedient to look through them and pull files from there.

In some cases, a file may be determined to be of low value, and so it may be worth deleting the record.

Geo itself is an excellent mitigation for files missing on the primary. If a file disappears on the primary but it was already synced to the secondary, you can grab the secondary's file. In cases like this, the File is not checksummable error message does not occur on Geo secondary sites, and only the primary logs this error message.

This problem is more likely to show up in Geo secondary sites which were set up long after the original GitLab site. In this case, Geo is only surfacing an existing problem.

This behavior affects only the following data types through GitLab 14.6:

Data type	From version
Package Registry	13.10
Pipeline Artifacts	13.11
Terraform State Versions	13.12
Infrastructure Registry	14.0
External MR diffs	14.6
LFS Objects	14.6
Pages Deployments	14.6
Uploads	14.6
CI Job Artifacts	14.6

Since GitLab 14.7, files that are missing on the primary site are now treated as sync failures to make Geo visibly surface data loss risks. The sync/verification loop is therefore short-circuited. last_sync_failure is now set to The file is missing on the Geo primary site.

Failed syncs with GitLab-managed object storage replication

There is an issue in GitLab 14.2 through 14.7 that affects Geo when the GitLab-managed object storage replication is used, causing blob object types to fail synchronization.

Since GitLab 14.2, verification failures result in synchronization failures and cause a re-synchronization of these objects.

As verification is not implemented for files stored in object storage (see issue 13845 for more details), this results in a loop that consistently fails for all objects stored in object storage.

You can work around this by marking the objects as synced and succeeded verification, however be aware that can also mark objects that may be missing from the primary.

To do that, enter the Rails console and run:

Gitlab::Geo.verification_enabled_replicator_classes.each do |klass|
  updated = klass.registry_class.failed.where(last_sync_failure: "Verification failed with: Error during verification: File is not checksummable").update_all(verification_checksum: '0000000000000000000000000000000000000000', verification_state: 2, verification_failure: nil, verification_retry_at: nil, state: 2, last_sync_failure: nil, retry_at: nil, verification_retry_count: 0, retry_count: 0)
  pp "Updated #{updated} #{klass.replicable_name_plural}"
end

Message: curl 18 transfer closed with outstanding read data remaining & fetch-pack: unexpected disconnect while reading sideband packet

Unstable networking conditions can cause Gitaly to fail when trying to fetch large repository data from the primary site. This is more likely to happen if a repository has to be replicated from scratch between sites.

Geo retries several times, but if the transmission is consistently interrupted by network hiccups, an alternative method such as rsync can be used to circumvent git and create the initial copy of any repository that fails to be replicated by Geo.

We recommend transferring each failing repository individually and checking for consistency after each transfer. Follow the single target rsync instructions to transfer each affected repository from the primary to the secondary site.

Fixing errors during a failover or when promoting a secondary to a primary node

The following are possible error messages that might be encountered during failover or when promoting a secondary to a primary node with strategies to resolve them.

Message: ActiveRecord::RecordInvalid: Validation failed: Name has already been taken

When promoting a secondary site, you might encounter the following error message:

Running gitlab-rake geo:set_secondary_as_primary...

rake aborted!
ActiveRecord::RecordInvalid: Validation failed: Name has already been taken
/opt/gitlab/embedded/service/gitlab-rails/ee/lib/tasks/geo.rake:236:in `block (3 levels) in <top (required)>'
/opt/gitlab/embedded/service/gitlab-rails/ee/lib/tasks/geo.rake:221:in `block (2 levels) in <top (required)>'
/opt/gitlab/embedded/bin/bundle:23:in `load'
/opt/gitlab/embedded/bin/bundle:23:in `<main>'
Tasks: TOP => geo:set_secondary_as_primary
(See full trace by running task with --trace)

You successfully promoted this node!

If you encounter this message when running gitlab-rake geo:set_secondary_as_primary or gitlab-ctl promote-to-primary-node, either:

• Enter a Rails console and run:

  Rails.application.load_tasks; nil
  Gitlab::Geo.expire_cache!
  Rake::Task['geo:set_secondary_as_primary'].invoke
  

• Upgrade to GitLab 12.6.3 or later if it is safe to do so. For example, if the failover was just a test. A caching-related bug was fixed.

Message: ActiveRecord::RecordInvalid: Validation failed: Enabled Geo primary node cannot be disabled

If you disabled a secondary node, either with the replication pause task (GitLab 13.2) or by using the user interface (GitLab 13.1 and earlier), you must first re-enable the node before you can continue. This is fixed in GitLab 13.4.

This can be fixed in the database.

1. Start a database console:

   In GitLab 14.2 and later:

   sudo gitlab-rails dbconsole --database main
   

   In GitLab 14.1 and earlier:

   sudo gitlab-rails dbconsole
   

2. Run the following command, replacing https://<secondary url>/ with the URL for your secondary server. You can use either http or https, but ensure that you end the URL with a slash (/):

   UPDATE geo_nodes SET enabled = true WHERE url = 'https://<secondary url>/' AND enabled = false;"
   

   This should update one row.

Message: NoMethodError: undefined method `secondary?' for nil:NilClass

When promoting a secondary site, you might encounter the following error message:

sudo gitlab-rake geo:set_secondary_as_primary

rake aborted!
NoMethodError: undefined method `secondary?' for nil:NilClass
/opt/gitlab/embedded/service/gitlab-rails/ee/lib/tasks/geo.rake:232:in `block (3 levels) in <top (required)>'
/opt/gitlab/embedded/service/gitlab-rails/ee/lib/tasks/geo.rake:221:in `block (2 levels) in <top (required)>'
/opt/gitlab/embedded/bin/bundle:23:in `load'
/opt/gitlab/embedded/bin/bundle:23:in `<main>'
Tasks: TOP => geo:set_secondary_as_primary
(See full trace by running task with --trace)

This command is intended to be executed on a secondary site only, and this error message is displayed if you attempt to run this command on a primary site.

Message: sudo: gitlab-pg-ctl: command not found

When promoting a secondary site with multiple nodes, you need to run the gitlab-pg-ctl command to promote the PostgreSQL read-replica database.

In GitLab 12.8 and earlier, this command fails with the message:

sudo: gitlab-pg-ctl: command not found

In this case, the workaround is to use the full path to the binary, for example:

sudo /opt/gitlab/embedded/bin/gitlab-pg-ctl promote

GitLab 12.9 and later are unaffected by this error message.

Message: ERROR - Replication is not up-to-date during gitlab-ctl promotion-preflight-checks

In GitLab 13.7 and earlier, if you have a data type with zero items to sync, this command reports ERROR - Replication is not up-to-date even if replication is actually up-to-date. This bug was fixed in GitLab 13.8 and later.

Message: ERROR - Replication is not up-to-date during gitlab-ctl promote-to-primary-node

In GitLab 13.7 and earlier, if you have a data type with zero items to sync, this command reports ERROR - Replication is not up-to-date even if replication is actually up-to-date. If replication and verification output shows that it is complete, you can add --skip-preflight-checks to make the command complete promotion. This bug was fixed in GitLab 13.8 and later.

Errors when using --skip-preflight-checks or --force

In GitLab 13.4 and earlier, you could receive one of the following error messages when using --skip-preflight-checks or --force:

get_ctl_options': invalid option: --skip-preflight-checks (OptionParser::InvalidOption)

get_ctl_options': invalid option: --force (OptionParser::InvalidOption)

This can happen with XFS or file systems that list files in lexical order, because the load order of the Omnibus GitLab command files can be different than expected, and a global function would get redefined. More details can be found in the related issue.

The workaround is to manually run the preflight checks and promote the database, by running the following commands on the Geo secondary site:

sudo gitlab-ctl promotion-preflight-checks
sudo /opt/gitlab/embedded/bin/gitlab-pg-ctl promote
sudo gitlab-ctl reconfigure
sudo gitlab-rake geo:set_secondary_as_primary

Expired artifacts

If you notice for some reason there are more artifacts on the Geo secondary node than on the Geo primary node, you can use the Rake task to cleanup orphan artifact files.

On a Geo secondary node, this command also cleans up all Geo registry record related to the orphan files on disk.

Fixing sign in errors

Message: The redirect URI included is not valid

If you are able to sign in to the primary node, but you receive this error message when attempting to sign in to a secondary, you should verify the Geo node's URL matches its external URL.

On the primary node:

1. On the top bar, select Menu > Admin.
2. On the left sidebar, select Geo > Nodes.
3. Find the affected secondary site and select Edit.
4. Ensure the URL field matches the value found in /etc/gitlab/gitlab.rb in external_url "https://gitlab.example.com" on the frontend servers of the secondary node.

Fixing common errors

This section documents common error messages reported in the Admin Area, and how to fix them.

Geo database configuration file is missing

GitLab cannot find or doesn't have permission to access the database_geo.yml configuration file.

In an Omnibus GitLab installation, the file should be in /var/opt/gitlab/gitlab-rails/etc. If it doesn't exist or inadvertent changes have been made to it, run sudo gitlab-ctl reconfigure to restore it to its correct state.

If this path is mounted on a remote volume, ensure your volume configuration has the correct permissions.

An existing tracking database cannot be reused

Geo cannot reuse an existing tracking database.

It is safest to use a fresh secondary, or reset the whole secondary by following Resetting Geo secondary node replication.

Geo node has a database that is writable which is an indication it is not configured for replication with the primary node

This error message refers to a problem with the database replica on a secondary node, which Geo expects to have access to. It usually means, either:

• An unsupported replication method was used (for example, logical replication).
• The instructions to set up a Geo database replication were not followed correctly.
• Your database connection details are incorrect, that is you have specified the wrong user in your /etc/gitlab/gitlab.rb file.

Geo secondary sites require two separate PostgreSQL instances:

• A read-only replica of the primary node.
• A regular, writable instance that holds replication metadata. That is, the Geo tracking database.

This error message indicates that the replica database in the secondary site is misconfigured and replication has stopped.

To restore the database and resume replication, you can do one of the following:

• Reset the Geo secondary site replication.
• Set up a new secondary Geo Omnibus instance.

If you set up a new secondary from scratch, you must also remove the old site from the Geo cluster.

Geo node does not appear to be replicating the database from the primary node

The most common problems that prevent the database from replicating correctly are:

• Secondary nodes cannot reach the primary node. Check credentials, firewall rules, and so on.
• SSL certificate problems. Make sure you copied /etc/gitlab/gitlab-secrets.json from the primary node.
• Database storage disk is full.
• Database replication slot is misconfigured.
• Database is not using a replication slot or another alternative and cannot catch-up because WAL files were purged.

Make sure you follow the Geo database replication instructions for supported configuration.

Geo database version (...) does not match latest migration (...)

If you are using Omnibus GitLab installation, something might have failed during upgrade. You can:

• Run sudo gitlab-ctl reconfigure.
• Manually trigger the database migration by running: sudo gitlab-rake db:migrate:geo as root on the secondary node.

GitLab indicates that more than 100% of repositories were synced

This can be caused by orphaned records in the project registry. You can clear them using a Rake task.

Geo Admin Area returns 404 error for a secondary node

Sometimes sudo gitlab-rake gitlab:geo:check indicates that the secondary node is healthy, but a 404 Not Found error message for the secondary node is returned in the Geo Admin Area on the primary node.

To resolve this issue:

• Try restarting the secondary using sudo gitlab-ctl restart.
• Check /var/log/gitlab/gitlab-rails/geo.log to see if the secondary node is using IPv6 to send its status to the primary node. If it is, add an entry to the primary node using IPv4 in the /etc/hosts file. Alternatively, you should enable IPv6 on the primary node.

Secondary site returns 502 errors with Geo proxying

When Geo proxying for secondary sites is enabled, and the secondary site user interface returns 502 errors, it is possible that the response header proxied from the primary site is too large.

Check the NGINX logs for errors similar to this example:

2022/01/26 00:02:13 [error] 26641#0: *829148 upstream sent too big header while reading response header from upstream, client: 1.2.3.4, server: geo.staging.gitlab.com, request: "POST /users/sign_in HTTP/2.0", upstream: "http://unix:/var/opt/gitlab/gitlab-workhorse/sockets/socket:/users/sign_in", host: "geo.staging.gitlab.com", referrer: "https://geo.staging.gitlab.com/users/sign_in"

To resolve this issue:

1. Set nginx['proxy_custom_buffer_size'] = '8k' in /etc/gitlab.rb on all web nodes on the secondary site.
2. Reconfigure the secondary using sudo gitlab-ctl reconfigure.

If you still get this error, you can further increase the buffer size by repeating the steps above and changing the 8k size, for example by doubling it to 16k.

Geo Admin Area shows 'Unknown' for health status and 'Request failed with status code 401'

If using a load balancer, ensure that the load balancer's URL is set as the external_url in the /etc/gitlab/gitlab.rb of the nodes behind the load balancer.

Geo Admin Area shows 'Unhealthy' after enabling Maintenance Mode

In GitLab 13.9 through GitLab 14.3, when GitLab Maintenance Mode is enabled, the status of Geo secondary sites stops getting updated. After 10 minutes, the status changes to Unhealthy.

Geo secondary sites continue to replicate and verify data, and the secondary sites should still be usable. You can use the Sync status Rake task to determine the actual status of a secondary site during Maintenance Mode.

This bug was fixed in GitLab 14.4.

Primary site returns 500 error when accessing /admin/geo/replication/projects

Navigating to Admin > Geo > Replication (or /admin/geo/replication/projects) on a primary Geo site, shows a 500 error, while that same link on the secondary works fine. The primary's production.log has a similar entry to the following:

Geo::TrackingBase::SecondaryNotConfigured: Geo secondary database is not configured
  from ee/app/models/geo/tracking_base.rb:26:in `connection'
  [..]
  from ee/app/views/admin/geo/projects/_all.html.haml:1

On a Geo primary site this error can be ignored.

This happens because GitLab is attempting to display registries from the Geo tracking database which doesn't exist on the primary site (only the original projects exist on the primary; no replicated projects are present, therefore no tracking database exists).

Secondary site returns 400 error "Request header or cookie too large"

This error can happen when the internal URL of the primary site is incorrect.

For example, when you use a unified URL and the primary site's internal URL is also equal to the external URL. This causes a loop when a secondary site proxies requests to the primary site's internal URL.

To fix this issue, set the primary site's internal URL to a URL that is:

• Unique to the primary site.
• Accessible from all secondary sites.

1. Enter the Rails console on the primary site.

2. Run the following, replacing https://unique.url.for.primary.site with your specific internal URL. For example, depending on your network configuration, you could use an IP address, like http://1.2.3.4.

   GeoNode.where(primary: true).first.update!(internal_url: "https://unique.url.for.primary.site")
   

Fixing client errors

Authorization errors from LFS HTTP(S) client requests

You may have problems if you're running a version of Git LFS before 2.4.2. As noted in this authentication issue, requests redirected from the secondary to the primary node do not properly send the Authorization header. This may result in either an infinite Authorization <-> Redirect loop, or Authorization error messages.

Error: Net::ReadTimeout when pushing through SSH on a Geo secondary

When you push large repositories through SSH on a Geo secondary site, you may encounter a timeout. This is because Rails proxies the push to the primary and has a 60 second default timeout, as described in this Geo issue.

Current workarounds are:

• Push through HTTP instead, where Workhorse proxies the request to the primary (or redirects to the primary if Geo proxying is not enabled).
• Push directly to the primary.

Example log (gitlab-shell.log):

Failed to contact primary https://primary.domain.com/namespace/push_test.git\\nError: Net::ReadTimeout\",\"result\":null}" code=500 method=POST pid=5483 url="http://127.0.0.1:3000/api/v4/geo/proxy_git_push_ssh/push"

Recovering from a partial failover

The partial failover to a secondary Geo site may be the result of a temporary/transient issue. Therefore, first attempt to run the promote command again.

1. SSH into every Sidekiq, PostgresSQL, Gitaly, and Rails node in the secondary site and run one of the following commands:

   • To promote the secondary node to primary:

     sudo gitlab-ctl geo promote
     

   • To promote the secondary node to primary without any further confirmation:

     sudo gitlab-ctl geo promote --force
     

2. Verify you can connect to the newly-promoted primary site using the URL used previously for the secondary site.

3. If successful, the secondary site is now promoted to the primary site.

If the above steps are not successful, proceed through the next steps:

1. SSH to every Sidekiq, PostgresSQL, Gitaly and Rails node in the secondary site and perform the following operations:

   • Create a /etc/gitlab/gitlab-cluster.json file with the following content:

     {
       "primary": true,
       "secondary": false
     }
     

   • Reconfigure GitLab for the changes to take effect:

     sudo gitlab-ctl reconfigure
     

2. Verify you can connect to the newly-promoted primary site using the URL used previously for the secondary site.

3. If successful, the secondary site is now promoted to the primary site.