Integrity check Rake task

GitLab provides Rake tasks to check the integrity of various components.

Repository integrity

Even though Git is very resilient and tries to prevent data integrity issues, there are times when things go wrong. The following Rake tasks intend to help GitLab administrators diagnose problem repositories so they can be fixed.

There are 3 things that are checked to determine integrity.

  1. Git repository file system check (git fsck). This step verifies the connectivity and validity of objects in the repository.
  2. Check for config.lock in the repository directory.
  3. Check for any branch/references lock files in refs/heads.

It’s important to note that the existence of config.lock or reference locks alone do not necessarily indicate a problem. Lock files are routinely created and removed as Git and GitLab perform operations on the repository. They serve to prevent data integrity issues. However, if a Git operation is interrupted these locks may not be cleaned up properly.

The following symptoms may indicate a problem with repository integrity. If users experience these symptoms you may use the Rake tasks described below to determine exactly which repositories are causing the trouble.

  • Receiving an error when trying to push code - remote: error: cannot lock ref
  • A 500 error when viewing the GitLab dashboard or when accessing a specific project.

Check project code repositories

This task loops through the project code repositories and runs the integrity check described previously. If a project uses a pool repository, that will also be checked. Other types of Git repositories are not checked.

Omnibus Installation 

sudo gitlab-rake gitlab:git:fsck

Source Installation 

sudo -u git -H bundle exec rake gitlab:git:fsck RAILS_ENV=production

Checksum of repository refs

One Git repository can be compared to another by checksumming all refs of each repository. If both repositories have the same refs, and if both repositories pass an integrity check, then we can be confident that both repositories are the same.

For example, this can be used to compare a backup of a repository against the source repository.

Check all GitLab repositories

This task loops through all repositories on the GitLab server and outputs checksums in the format <PROJECT ID>,<CHECKSUM>.

  • If a repository doesn’t exist, the project ID will have a blank checksum.
  • If a repository exists but is empty, the output checksum is 0000000000000000000000000000000000000000.
  • Projects which don’t exist are skipped.

Omnibus Installation 

sudo gitlab-rake gitlab:git:checksum_projects

Source Installation 

sudo -u git -H bundle exec rake gitlab:git:checksum_projects RAILS_ENV=production

For example, if:

  • Project with ID#2 doesn’t exist, it will be skipped.
  • Project with ID#4 doesn’t have a repository, its checksum will be blank.
  • Project with ID#5 has an empty repository, its checksum will be 0000000000000000000000000000000000000000.

The output would then look something like: 

1,cfa3f06ba235c13df0bb28e079bcea62c5848af2
3,3f3fb58a8106230e3a6c6b48adc2712fb3b6ef87
4,
5,0000000000000000000000000000000000000000
6,6c6b48adc2712fb3b6ef87cfa3f06ba235c13df0

Check specific GitLab repositories

Optionally, specific project IDs can be checksummed by setting an environment variable CHECKSUM_PROJECT_IDS with a list of comma-separated integers, for example: 

CHECKSUM_PROJECT_IDS="1,3" sudo gitlab-rake gitlab:git:checksum_projects

Uploaded files integrity

Various types of files can be uploaded to a GitLab installation by users. These integrity checks can detect missing files. Additionally, for locally stored files, checksums are generated and stored in the database upon upload, and these checks verify them against current files.

Currently, integrity checks are supported for the following types of file:

  • CI artifacts (Available from version 10.7.0)
  • LFS objects (Available from version 10.6.0)
  • User uploads (Available from version 10.6.0)

Omnibus Installation 

sudo gitlab-rake gitlab:artifacts:check
sudo gitlab-rake gitlab:lfs:check
sudo gitlab-rake gitlab:uploads:check

Source Installation 

sudo -u git -H bundle exec rake gitlab:artifacts:check RAILS_ENV=production
sudo -u git -H bundle exec rake gitlab:lfs:check RAILS_ENV=production
sudo -u git -H bundle exec rake gitlab:uploads:check RAILS_ENV=production

These tasks also accept some environment variables which you can use to override certain values:

Variable Type Description
BATCH integer Specifies the size of the batch. Defaults to 200.
ID_FROM integer Specifies the ID to start from, inclusive of the value.
ID_TO integer Specifies the ID value to end at, inclusive of the value.
VERBOSE boolean Causes failures to be listed individually, rather than being summarized. 
sudo gitlab-rake gitlab:artifacts:check BATCH=100 ID_FROM=50 ID_TO=250
sudo gitlab-rake gitlab:lfs:check BATCH=100 ID_FROM=50 ID_TO=250
sudo gitlab-rake gitlab:uploads:check BATCH=100 ID_FROM=50 ID_TO=250

Example output: 

$ sudo gitlab-rake gitlab:uploads:check
Checking integrity of Uploads
- 1..1350: Failures: 0
- 1351..2743: Failures: 0
- 2745..4349: Failures: 2
- 4357..5762: Failures: 1
- 5764..7140: Failures: 2
- 7142..8651: Failures: 0
- 8653..10134: Failures: 0
- 10135..11773: Failures: 0
- 11777..13315: Failures: 0
Done!

Example verbose output: 

$ sudo gitlab-rake gitlab:uploads:check VERBOSE=1
Checking integrity of Uploads
- 1..1350: Failures: 0
- 1351..2743: Failures: 0
- 2745..4349: Failures: 2
  - Upload: 3573: #<Errno::ENOENT: No such file or directory @ rb_sysopen - /opt/gitlab/embedded/service/gitlab-rails/public/uploads/user-foo/project-bar/7a77cc52947bfe188adeff42f890bb77/image.png>
  - Upload: 3580: #<Errno::ENOENT: No such file or directory @ rb_sysopen - /opt/gitlab/embedded/service/gitlab-rails/public/uploads/user-foo/project-bar/2840ba1ba3b2ecfa3478a7b161375f8a/pug.png>
- 4357..5762: Failures: 1
  - Upload: 4636: #<Google::Apis::ServerError: Server error>
- 5764..7140: Failures: 2
  - Upload: 5812: #<NoMethodError: undefined method `hashed_storage?' for nil:NilClass>
  - Upload: 5837: #<NoMethodError: undefined method `hashed_storage?' for nil:NilClass>
- 7142..8651: Failures: 0
- 8653..10134: Failures: 0
- 10135..11773: Failures: 0
- 11777..13315: Failures: 0
Done!

LDAP check

The LDAP check Rake task tests the bind DN and password credentials (if configured) and lists a sample of LDAP users. This task is also executed as part of the gitlab:check task, but can run independently. See LDAP Rake Tasks - LDAP Check for details.

Troubleshooting

The following are solutions to problems you might discover using the Rake tasks documented above.

Dangling commits

gitlab:git:fsck can find dangling commits. To fix them, try enabling housekeeping.

If the issue persists, try triggering gc via the Rails Console: 

p = Project.find_by_path("project-name")
Repositories::HousekeepingService.new(p, :gc).execute

Delete references to missing remote uploads

gitlab-rake gitlab:uploads:check VERBOSE=1 detects remote objects that do not exist because they were deleted externally but their references still exist in the GitLab database.

Example output with error message: 

$ sudo gitlab-rake gitlab:uploads:check VERBOSE=1
Checking integrity of Uploads
- 100..434: Failures: 2
- Upload: 100: Remote object does not exist
- Upload: 101: Remote object does not exist
Done!

To delete these references to remote uploads that were deleted externally, open the GitLab Rails Console and run: 

uploads_deleted=0
Upload.find_each do |upload|
  next if upload.retrieve_uploader.file.exists?
  uploads_deleted=uploads_deleted + 1
  p upload                            ### allow verification before destroy
  # p upload.destroy!                 ### uncomment to actually destroy
end
p "#{uploads_deleted} remote objects were destroyed."

Delete references to missing artifacts

gitlab-rake gitlab:artifacts:check VERBOSE=1 detects when artifacts (or job.log files):

  • Are deleted outside of GitLab.
  • Have references still in the GitLab database.

When this scenario is detected, the Rake task displays an error message. For example: 

Checking integrity of Job artifacts
- 3..8: Failures: 2
  - Job artifact: 3: #<Errno::ENOENT: No such file or directory @ rb_sysopen - /var/opt/gitlab/gitlab-rails/shared/artifacts/4e/07/4e07408562bedb8b60ce05c1decfe3ad16b72230967de01f640b7e4729b49fce/2021_05_26/5/3/job.log>
  - Job artifact: 8: #<Errno::ENOENT: No such file or directory @ rb_sysopen - /var/opt/gitlab/gitlab-rails/shared/artifacts/4e/07/4e07408562bedb8b60ce05c1decfe3ad16b72230967de01f640b7e4729b49fce/2021_05_26/6/8/job.log>
Done!

To delete these references to missing local artifacts (job.log files):

  1. Open the GitLab Rails Console.

  2. Run the following Ruby code: 

    artifacts_deleted = 0
::Ci::JobArtifact.all.each do |artifact|                       ### Iterate artifacts
#  next if artifact.file.filename != "job.log"                 ### Uncomment if only `job.log` files' references are to be processed
  next if artifact.file.exists?                                ### Skip if the file reference is valid
  artifacts_deleted += 1
  puts "#{artifact.id}  #{artifact.file.path} is missing."     ### Allow verification before destroy
#  artifact.destroy!                                           ### Uncomment to actually destroy
end
puts "Count of identified/destroyed invalid references: #{artifacts_deleted}"

Delete references to missing LFS objects

If gitlab-rake gitlab:lfs:check VERBOSE=1 detects LFS objects that exist in the database but not on disk, follow the procedure in the LFS documentation to remove the database entries.