Troubleshooting Geo synchronization and verification errors

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If you notice replication or verification failures in Admin > Geo > Sites or the Sync status Rake task, you can try to resolve the failures with the following general steps:

  1. Geo automatically retries failures. If the failures are new and few in number, or if you suspect the root cause is already resolved, then you can wait to see if the failures go away.
  2. If failures were present for a long time, then many retries have already occurred, and the interval between automatic retries has increased to up to 4 hours depending on the type of failure. If you suspect the root cause is already resolved, you can manually retry replication or verification to avoid the wait.
  3. If the failures persist, use the following sections to try to resolve them.

Manually retry replication or verification

A Geo data type is a specific class of data that is required by one or more GitLab features to store relevant information and is replicated by Geo to secondary sites.

Geo data type classes

  • Blob types:
    • Ci::JobArtifact
    • Ci::PipelineArtifact
    • Ci::SecureFile
    • LfsObject
    • MergeRequestDiff
    • Packages::PackageFile
    • PagesDeployment
    • Terraform::StateVersion
    • Upload
    • DependencyProxy::Manifest
    • DependencyProxy::Blob
  • Git Repository types:
    • DesignManagement::Repository
    • ProjectRepository
    • ProjectWikiRepository
    • SnippetRepository
    • GroupWikiRepository
  • Other types:
    • ContainerRepository

The main kinds of classes are Registry, Model, and Replicator. If you have an instance of one of these classes, you can get the others. The Registry and Model mostly manage PostgreSQL DB state. The Replicator knows how to replicate/verify (or it can call a service to do it): 

model_record = Packages::PackageFile.last
model_record.replicator.registry.replicator.model_record # just showing that these methods exist

With all this information, you can:

Resync and reverify individual components

You can force a resync and reverify individual items for all component types managed by the self-service framework using the UI. On the secondary site, visit Admin > Geo > Replication.

However, if this doesn’t work, you can perform the same action using the Rails console. The following sections describe how to use internal application commands in the Rails console to cause replication or verification for individual records synchronously or asynchronously.

Geo registry table models

In the context of GitLab Geo, a registry record refers to registry tables in the Geo tracking database. Each record tracks a single replicable in the main GitLab database, such as an LFS file, or a project Git repository. The Rails models that correspond to Geo registry tables that can be queried are:

  • Geo::CiSecureFileRegistry
  • Geo::ContainerRepositoryRegistry
  • Geo::DependencyProxyBlobRegistry
  • Geo::DependencyProxyManifestRegistry
  • Geo::JobArtifactRegistry
  • Geo::LfsObjectRegistry
  • Geo::MergeRequestDiffRegistry
  • Geo::PackageFileRegistry
  • Geo::PagesDeploymentRegistry
  • Geo::PipelineArtifactRegistry
  • Geo::ProjectWikiRepositoryRegistry
  • Geo::SnippetRepositoryRegistry
  • Geo::TerraformStateVersionRegistry
  • Geo::UploadRegistry

You can use Rails to perform basic troubleshooting. Troubleshooting steps vary depending on the object type.

For blob types

caution
Commands that change data can cause damage if not run correctly or under the right conditions. Always run commands in a test environment first and have a backup instance ready to restore.

Start a Rails console session on a secondary site.

Using the Packages::PackageFile component as an example:

  • Find registry records that failed to sync: 

    Geo::PackageFileRegistry.failed

  • Find registry records that are missing on the primary site: 

    Geo::PackageFileRegistry.where(last_sync_failure: 'The file is missing on the Geo primary site')

  • Resync a package file, synchronously, given an ID: 

    model_record = Packages::PackageFile.find(<id>)
model_record.replicator.sync

  • Resync a package file, synchronously, given a registry ID: 

    registry = Geo::PackageFileRegistry.find(<registry_id>)
registry.replicator.sync

  • Resync a package file, asynchronously, given a registry ID. Since GitLab 16.2, a component can be asynchronously replicated as follows: 

    registry = Geo::PackageFileRegistry.find(<registry_id>)
registry.replicator.enqueue_sync

  • Reverify a package file, asynchronously, given a registry ID. Since GitLab 16.2, a component can be asynchronously reverified as follows: 

    registry = Geo::PackageFileRegistry.find(<registry_id>)
registry.replicator.verify_async

For repository types

caution
Commands that change data can cause damage if not run correctly or under the right conditions. Always run commands in a test environment first and have a backup instance ready to restore.

Start a Rails console session on a secondary site.

Using the SnippetRepository component as an example:

  • Resync a snippet repository, synchronously, given an ID: 

    model_record = Geo::SnippetRepositoryRegistry.find(<id>)
model_record.replicator.sync

  • Resync a snippet repository, synchronously, given a registry ID: 

    registry = Geo::SnippetRepositoryRegistry.find(<registry_id>)
registry.replicator.sync

  • Since GitLab 16.2, a component can be asynchronously replicated. Resync a snippet repository, asynchronously, given a registry ID: 

    registry = Geo::SnippetRepositoryRegistry.find(<registry_id>)
registry.replicator.enqueue_sync

  • Since GitLab 16.2, a component can be asynchronously reverified. Reverify a snippet repository, asynchronously, given a registry ID: 

    registry = Geo::SnippetRepositoryRegistry.find(<registry_id>)
registry.replicator.verify_async

Resync and reverify multiple components

History
  • Bulk resync and reverify added in GitLab 16.5.
caution
Commands that change data can cause damage if not run correctly or under the right conditions. Always run commands in a test environment first and have a backup instance ready to restore.

The following sections describe how to use internal application commands in the Rails console to cause bulk replication or verification.

Reverify all components (or any SSF data type which supports verification)

You can reverify any data type that supports verification from the Rails console.

For example, to reverify the Upload class:

  1. SSH into a GitLab Rails node in the primary Geo site.
  2. Open the Rails console.

  3. Mark all uploads as pending verification: 

    Upload.verification_state_table_class.each_batch do |relation|
  relation.update_all(verification_state: 0)
end
  4. This causes the primary to start checksumming all Uploads.
  5. When a primary successfully checksums a record, then all secondaries recalculate the checksum as well, and they compare the values.

For other SSF data types replace Upload in the command above with the desired model class.

Verify blob files on the secondary manually

This iterates over all package files on the secondary, looking at the verification_checksum stored in the database (which came from the primary) and then calculate this value on the secondary to check if they match. This does not change anything in the UI. 

# Run on secondary
status = {}

Packages::PackageFile.find_each do |package_file|
  primary_checksum = package_file.verification_checksum
  secondary_checksum = Packages::PackageFile.sha256_hexdigest(package_file.file.path)
  verification_status = (primary_checksum == secondary_checksum)

  status[verification_status.to_s] ||= []
  status[verification_status.to_s] << package_file.id
end

# Count how many of each value we get
status.keys.each {|key| puts "#{key} count: #{status[key].count}"}

# See the output in its entirety
status

Failed verification of Uploads on the primary Geo site

If verification of some uploads is failing on the primary Geo site with verification_checksum = nil and with verification_failure containing Error during verification: undefined method `underscore' for NilClass:Class or The model which owns this Upload is missing., this is due to orphaned Uploads. The parent record owning the Upload (the upload’s “model”) has somehow been deleted, but the Upload record still exists. This is usually due to a bug in the application, introduced by implementing bulk delete of the “model” while forgetting to bulk delete its associated Upload records. These verification failures are therefore not failures to verify, rather, the errors are a result of bad data in Postgres.

You can find these errors in the geo.log file on the primary Geo site.

To confirm that model records are missing, you can run a Rake task on the primary Geo site: 

sudo gitlab-rake gitlab:uploads:check

You can delete these Upload records on the primary Geo site to get rid of these failures by running the following script from the Rails console: 

def delete_orphaned_uploads(dry_run: true)
  if dry_run
    p "This is a dry run. Upload rows will only be printed."
  else
    p "This is NOT A DRY RUN! Upload rows will be deleted from the DB!"
  end

  subquery = Geo::UploadState.where("(verification_failure LIKE 'Error during verification: The model which owns this Upload is missing.%' OR verification_failure = 'Error during verification: undefined method `underscore'' for NilClass:Class') AND verification_checksum IS NULL")
  uploads = Upload.where(upload_state: subquery)
  p "Found #{uploads.count} uploads with a model that does not exist"

  uploads_deleted = 0
  begin
    uploads.each do |upload|

      if dry_run
        p upload
      else
        uploads_deleted=uploads_deleted + 1
        p upload.destroy!
      end
    rescue => e
      puts "checking upload #{upload.id} failed with #{e.message}"
    end
  end

  p "#{uploads_deleted} remote objects were destroyed." unless dry_run
end

The above script defines a method named delete_orphaned_uploads which you can call like this to do a dry run: 

delete_orphaned_uploads(dry_run: true)

And to actually delete the orphaned upload rows: 

delete_orphaned_uploads(dry_run: false)

Message: "Error during verification","error":"File is not checksummable"

If you encounter these errors in your primary site geo.log, they’re also reflected in the UI under Admin > Geo > Sites. To remove those errors, you can identify the particular blob that generates the message so that you can inspect it.

  1. In a Puma or Sidekiq node in the primary site, open a Rails console.
  2. Run the following snippet to find the affected artifacts containing the File is not checksummable message:
note
The example provided below uses JobArtifact blob type; however, the same solution applies to any blob type that Geo uses.

artifacts = Ci::JobArtifact.verification_failed.where("verification_failure like '%File is not checksummable%'");1
puts "Found #{artifacts.count} artifacts that failed verification with 'File is not checksummable'. The first one:"
pp artifacts.first

If you determine that the affected files need to be recovered then you can explore these options (non-exhaustive) to recover the missing files:

  • Check if the secondary site has the object and manually copy them to the primary.
  • Look through old backups and manually copy the object back into the primary site.
  • Spot check some to try to determine that it’s probably fine to destroy the records, for example, if they are all very old artifacts, then maybe they are not critical data.

Often, these kinds of errors happen when a file is checksummed by Geo, and then goes missing from the primary site. After you identify the affected files, you should check the projects that the files belong to from the UI to decide if it’s acceptable to delete the file reference. If so, you can destroy the references with the following irreversible snippet: 

def destroy_artifacts_not_checksummable
  artifacts = Ci::JobArtifact.verification_failed.where("verification_failure like '%File is not checksummable%'");1
  puts "Found #{artifacts.count} artifacts that failed verification with 'File is not checksummable'."
  puts "Enter 'y' to continue: "
  prompt = STDIN.gets.chomp
  if prompt != 'y'
    puts "Exiting without action..."
    return
  end

  puts "Destroying all..."
  artifacts.destroy_all
end

destroy_artifacts_not_checksummable

Error: Error syncing repository: 13:fatal: could not read Username

The last_sync_failure error Error syncing repository: 13:fatal: could not read Username for 'https://gitlab.example.com': terminal prompts disabled indicates that JWT authentication is failing during a Geo clone or fetch request. See Geo (development) > Authentication for more context.

First, check that system clocks are synced. Run the Health check Rake task, or manually check that date, on all Sidekiq nodes on the secondary site and all Puma nodes on the primary site, are the same.

If system clocks are synced, then the JWT token may be expiring while Git fetch is performing calculations between its two separate HTTP requests. See issue 464101, which existed in all GitLab versions until it was fixed in GitLab 17.1.0, 17.0.5, and 16.11.7.

To validate if you are experiencing this issue:

  1. Monkey patch the code in a Rails console to increase the validity period of the token from 1 minute to 10 minutes. Run this in Rails console on the secondary site: 

    module Gitlab; module Geo; class BaseRequest
  private
  def geo_auth_token(message)
    signed_data = Gitlab::Geo::SignedData.new(geo_node: requesting_node, validity_period: 10.minutes).sign_and_encode_data(message)

    "#{GITLAB_GEO_AUTH_TOKEN_TYPE} #{signed_data}"
  end
end;end;end

  2. In the same Rails console, resync an affected project: 

    Project.find_by_full_path('<mygroup/mysubgroup/myproject>').replicator.resync

  3. Look at the sync state: 

    Project.find_by_full_path('<mygroup/mysubgroup/myproject>').replicator.registry

  4. If last_sync_failure no longer includes the error fatal: could not read Username, then you are affected by this issue. The state should now be 2, meaning “synced”. If so, then you should upgrade to a GitLab version with the fix. You may also wish to upvote or comment on issue 466681 which would have reduced the severity of this issue.

To workaround the issue, you must hot-patch all Sidekiq nodes in the secondary site to extend the JWT expiration time:

  1. Edit /opt/gitlab/embedded/service/gitlab-rails/ee/lib/gitlab/geo/signed_data.rb.

  2. Find Gitlab::Geo::SignedData.new(geo_node: requesting_node) and add , validity_period: 10.minutes to it: 

    - Gitlab::Geo::SignedData.new(geo_node: requesting_node)
+ Gitlab::Geo::SignedData.new(geo_node: requesting_node, validity_period: 10.minutes)

  3. Restart Sidekiq: 

    sudo gitlab-ctl restart sidekiq
  4. Unless you upgrade to a version containing the fix, you would have to repeat this workaround after every GitLab upgrade.

Error: fetch remote: signal: terminated: context deadline exceeded at exactly 3 hours

If Git fetch fails at exactly three hours while syncing a Git repository:

  1. Edit /etc/gitlab/gitlab.rb to increase the Git timeout from the default of 10800 seconds: 

    # Git timeout in seconds
gitlab_rails['gitlab_shell_git_timeout'] = 21600

  2. Reconfigure GitLab: 

    sudo gitlab-ctl reconfigure

Error Failed to open TCP connection to localhost:5000 on secondary when configuring registry replication

You may face the following error when configuring container registry replication on the secondary site: 

Failed to open TCP connection to localhost:5000 (Connection refused - connect(2) for \"localhost\" port 5000)"

It happens if the container registry is not enabled on the secondary site. To fix it, check that the container registry is enabled on the secondary site. Note that if Let’s Encrypt integration is disabled, container registry is disabled as well, and you must configure it manually.

Reverify all uploads (or any SSF data type which is verified)

  1. SSH into a GitLab Rails node in the primary Geo site.
  2. Open Rails console.
  3. Mark all uploads as “pending verification”:
caution
Commands that change data can cause damage if not run correctly or under the right conditions. Always run commands in a test environment first and have a backup instance ready to restore.

Reverify all uploads 

Upload.verification_state_table_class.each_batch do |relation|
  relation.update_all(verification_state: 0)
end

Reverify failed uploads only 

Upload.verification_state_table_class.where(verification_state: 3).each_batch do |relation|
  relation.update_all(verification_state: 0)
end

How the reverification process works

When you reverify all uploads or reverify failed uploads only:

  1. This causes the primary to start checksumming the Uploads depending on which commands were executed.
  2. When a primary successfully checksums a record, then all secondaries recalculate the checksum as well, and they compare the values.

You can perform a similar operation with other the Models handled by the Geo Self-Service Framework which have implemented verification:

  • LfsObject
  • MergeRequestDiff
  • Packages::PackageFile
  • Terraform::StateVersion
  • SnippetRepository
  • Ci::PipelineArtifact
  • PagesDeployment
  • Upload
  • Ci::JobArtifact
  • Ci::SecureFile
note
GroupWikiRepository is not in the previous list since verification is not implemented. There is an issue to implement this functionality in the Admin area UI.

Message: Synchronization failed - Error syncing repository

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

The following error message indicates a consistency check error when syncing the repository: 

Synchronization failed - Error syncing repository [..] fatal: fsck error in packed object

Several issues can trigger this error. For example, problems with email addresses: 

Error syncing repository: 13:fetch remote: "error: object <SHA>: badEmail: invalid author/committer line - bad email
   fatal: fsck error in packed object
   fatal: fetch-pack: invalid index-pack output

Another issue that can trigger this error is object <SHA>: hasDotgit: contains '.git'. Check the specific errors because you might have more than one problem across all your repositories.

A second synchronization error can also be caused by repository check issues: 

Error syncing repository: 13:Received RST_STREAM with error code 2.

These errors can be observed by immediately syncing all failed repositories.

Removing the malformed objects causing consistency errors involves rewriting the repository history, which is usually not an option.

To ignore these consistency checks, reconfigure Gitaly on the secondary Geo sites to ignore these git fsck issues. The following configuration example:

The Gitaly documentation has more details about other Git check failures and earlier versions of GitLab. 

gitaly['configuration'] = {
  git: {
    config: [
      { key: "fsck.duplicateEntries", value: "ignore" },
      { key: "fsck.badFilemode", value: "ignore" },
      { key: "fsck.missingEmail", value: "ignore" },
      { key: "fsck.badEmail", value: "ignore" },
      { key: "fsck.hasDotgit", value: "ignore" },
      { key: "fetch.fsck.duplicateEntries", value: "ignore" },
      { key: "fetch.fsck.badFilemode", value: "ignore" },
      { key: "fetch.fsck.missingEmail", value: "ignore" },
      { key: "fetch.fsck.badEmail", value: "ignore" },
      { key: "fetch.fsck.hasDotgit", value: "ignore" },
      { key: "receive.fsck.duplicateEntries", value: "ignore" },
      { key: "receive.fsck.badFilemode", value: "ignore" },
      { key: "receive.fsck.missingEmail", value: "ignore" },
      { key: "receive.fsck.badEmail", value: "ignore" },
      { key: "receive.fsck.hasDotgit", value: "ignore" },
    ],
  },
}

GitLab 16.1 and later include an enhancement that might resolve some of these issues.

Gitaly issue 5625 proposes to ensure that Geo replicates repositories even if the source repository contains problematic commits.

You can also get the error message Synchronization failed - Error syncing repository along with the following log messages. This error indicates that the expected Geo remote is not present in the .git/config file of a repository on the secondary Geo site’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 on the web interface for the secondary Geo site.

  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_project_registries = Geo::ProjectRepositoryRegistry.failed

if failed_project_registries.any?
  puts "Found #{failed_project_registries.count} failed project repository registry entries:"

  failed_project_registries.each do |registry|
    puts "ID: #{registry.id}, Project ID: #{registry.project_id}, Last Sync Failure: '#{registry.last_sync_failure}'"
  end
else
  puts "No failed project repository registry entries found."
end

  5. Run the following commands to execute a new sync for each project: 

    failed_project_registries.each do |registry|
  registry.replicator.sync
  puts "Sync initiated for registry ID: #{registry.id}, Project ID: #{registry.project_id}"
end

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.

Message: 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. Those conditions can result in this error: 

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

This error 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.

Project or project wiki repositories

Resync all Geo-replicable objects

You can schedule a full resync or reverification of all Geo-replicable objects from the UI:

  1. On the left sidebar, at the bottom, select Admin.
  2. Select Geo > Sites.
  3. Under Replication details, select the desired object.
  4. Select Resync all or Reverify all.

Alternatively, start a Rails console session on the secondary Geo site to gather more information, or execute these operations manually using the snippets below.

caution
Commands that change data can cause damage if not run correctly or under the right conditions. Always run commands in a test environment first and have a backup instance ready to restore.

Find repository verification failures

Get the number of verification failed repositories 

Geo::ProjectRepositoryRegistry.verification_failed.count

Find the verification failed repositories 

Geo::ProjectRepositoryRegistry.verification_failed

Find repositories that failed to sync 

Geo::ProjectRepositoryRegistry.failed

Mark all repositories for reverification

The following snippet marks all project repositories for reverification. After a minute or two, the system should begin to schedule Sidekiq jobs according to your concurrency limits: 

Geo::ProjectRepositoryRegistry.update_all(verification_state: 0)

If there’s a very large number of repositories to reverify, the single update query can time out. If this happens, you should run update queries in batches of rows using the same code as the Reverify all feature in the admin area: 

::Geo::RegistryBulkUpdateService.new(:reverify_all, Geo::ProjectRepositoryRegistry).execute

Resync project and project wiki repositories

Queue up all repositories for resync

The following snippet marks all project repositories for reverification. After a minute or two, the system should begin to schedule Sidekiq jobs according to your concurrency limits: 

Geo::ProjectRepositoryRegistry.update_all(state: 0, last_synced_at: nil)

If there’s a very large number of repositories to reverify, the single update query can time out. If this happens, you should run update queries in batches of rows using the same code as the Reverify all feature in the admin area: 

::Geo::RegistryBulkUpdateService.new(:resync_all, Geo::ProjectRepositoryRegistry).execute

Sync individual repository now 

project = Project.find_by_full_path('<group/project>')

project.replicator.sync

Sync all failed repositories now

The following script:

  • Loops over all failed repositories.
  • Displays the project details and the reasons for the last failure.
  • Attempts to resync the repository.
  • Reports back if a failure occurs, and why.
  • Might take some time to complete. Each repository check must complete before reporting back the result. If your session times out, take measures to allow the process to continue running such as starting a screen session, or running it using Rails runner and nohup. 
Geo::ProjectRepositoryRegistry.failed.find_each do |registry|
   begin
     puts "ID: #{registry.id}, Project ID: #{registry.project_id}, Last Sync Failure: '#{registry.last_sync_failure}'"
     registry.replicator.sync
     puts "Sync initiated for registry ID: #{registry.id}"
   rescue => e
     puts "ID: #{registry.id}, Project ID: #{registry.project_id}, Failed: '#{e}'", e.backtrace.join("\n")
   end
end ; nil

Find repository check failures in a Geo secondary site

note
All repositories data types have been migrated to the Geo Self-Service Framework in GitLab 16.3. There is an issue to implement this functionality back in the Geo Self-Service Framework.

For GitLab 16.2 and earlier:

When enabled for all projects, Repository checks are also performed on Geo secondary sites. The metadata is stored in the Geo tracking database.

Repository check failures on a Geo secondary site do not necessarily imply a replication problem. Here is a general approach to resolve these failures.

  1. Find affected repositories as mentioned below, as well as their logged errors.
  2. Try to diagnose specific git fsck errors. The range of possible errors is wide, try putting them into search engines.
  3. Test typical functions of the affected repositories. Pull from the secondary, view the files.
  4. Check if the primary site’s copy of the repository has an identical git fsck error. If you are planning a failover, then consider prioritizing that the secondary site has the same information that the primary site has. Ensure you have a backup of the primary, and follow planned failover guidelines.
  5. Push to the primary and check if the change gets replicated to the secondary site.
  6. If replication is not automatically working, try to manually sync the repository.

Start a Rails console session to enact the following, basic troubleshooting steps.

caution
Commands that change data can cause damage if not run correctly or under the right conditions. Always run commands in a test environment first and have a backup instance ready to restore.

Get the number of repositories that failed the repository check 

Geo::ProjectRegistry.where(last_repository_check_failed: true).count

Find the repositories that failed the repository check 

Geo::ProjectRegistry.where(last_repository_check_failed: true)

Resetting Geo secondary site replication

If you get a secondary site 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 Log Cursor.

    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. Clear Gitaly/Gitaly Cluster data.

    Gitaly
    mv /var/opt/gitlab/git-data/repositories /var/opt/gitlab/git-data/repositories.old
sudo gitlab-ctl reconfigure
    Gitaly Cluster
    1. Optional. Disable the Praefect internal load balancer.

    2. Stop Praefect on each Praefect server: 

      sudo gitlab-ctl stop praefect

    3. Reset the Praefect database: 

      sudo /opt/gitlab/embedded/bin/psql -U praefect -d template1 -h localhost -c "DROP DATABASE praefect_production WITH (FORCE);"
sudo /opt/gitlab/embedded/bin/psql -U praefect -d template1 -h localhost -c "CREATE DATABASE praefect_production WITH OWNER=praefect ENCODING=UTF8;"

    4. Rename/delete repository data from each Gitaly node: 

      sudo mv /var/opt/gitlab/git-data/repositories /var/opt/gitlab/git-data/repositories.old
sudo gitlab-ctl reconfigure

    5. On your Praefect deploy node run reconfigure to set up the database: 

      sudo gitlab-ctl reconfigure

    6. Start Praefect on each Praefect server: 

      sudo gitlab-ctl start praefect
    7. Optional. If you disabled it, reactivate the Praefect internal load balancer.
    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.

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

    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.

    caution
    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