Troubleshooting Gitaly and Gitaly Cluster (FREE SELF)

Refer to the information below when troubleshooting Gitaly and Gitaly Cluster.

Troubleshoot Gitaly

The following sections provide possible solutions to Gitaly errors.

See also Gitaly timeout settings, and our advice on parsing the gitaly/current file.

Check versions when using standalone Gitaly servers

When using standalone Gitaly servers, you must make sure they are the same version as GitLab to ensure full compatibility:

1. On the top bar, select Menu > Admin on your GitLab instance.
2. On the left sidebar, select Overview > Gitaly Servers.
3. Confirm all Gitaly servers indicate that they are up to date.

Use gitaly-debug

The gitaly-debug command provides "production debugging" tools for Gitaly and Git performance. It is intended to help production engineers and support engineers investigate Gitaly performance problems.

If you're using GitLab 11.6 or newer, this tool should be installed on your GitLab or Gitaly server already at /opt/gitlab/embedded/bin/gitaly-debug. If you're investigating an older GitLab version you can compile this tool offline and copy the executable to your server:

git clone https://gitlab.com/gitlab-org/gitaly.git
cd cmd/gitaly-debug
GOOS=linux GOARCH=amd64 go build -o gitaly-debug

To see the help page of gitaly-debug for a list of supported sub-commands, run:

gitaly-debug -h

Commits, pushes, and clones return a 401

remote: GitLab: 401 Unauthorized

You need to sync your gitlab-secrets.json file with your GitLab application nodes.

Client side gRPC logs

Gitaly uses the gRPC RPC framework. The Ruby gRPC client has its own log file which may contain useful information when you are seeing Gitaly errors. You can control the log level of the gRPC client with the GRPC_LOG_LEVEL environment variable. The default level is WARN.

You can run a gRPC trace with:

sudo GRPC_TRACE=all GRPC_VERBOSITY=DEBUG gitlab-rake gitlab:gitaly:check

Server side gRPC logs

gRPC tracing can also be enabled in Gitaly itself with the GODEBUG=http2debug environment variable. To set this in an Omnibus GitLab install:

1. Add the following to your gitlab.rb file:

   gitaly['env'] = {
     "GODEBUG=http2debug" => "2"
   }

2. Reconfigure GitLab.

Correlating Git processes with RPCs

Sometimes you need to find out which Gitaly RPC created a particular Git process.

One method for doing this is by using DEBUG logging. However, this needs to be enabled ahead of time and the logs produced are quite verbose.

A lightweight method for doing this correlation is by inspecting the environment of the Git process (using its PID) and looking at the CORRELATION_ID variable:

PID=<Git process ID>
sudo cat /proc/$PID/environ | tr '\0' '\n' | grep ^CORRELATION_ID=

This method isn't reliable for git cat-file processes, because Gitaly internally pools and re-uses those across RPCs.

Observing gitaly-ruby traffic

gitaly-ruby is an internal implementation detail of Gitaly, so, there's not that much visibility into what goes on inside gitaly-ruby processes.

If you have Prometheus set up to scrape your Gitaly process, you can see request rates and error codes for individual RPCs in gitaly-ruby by querying grpc_client_handled_total.

• In theory, this metric does not differentiate between gitaly-ruby and other RPCs.
• In practice from GitLab 11.9, all gRPC calls made by Gitaly itself are internal calls from the main Gitaly process to one of its gitaly-ruby sidecars.

Assuming your grpc_client_handled_total counter only observes Gitaly, the following query shows you RPCs are (most likely) internally implemented as calls to gitaly-ruby:

sum(rate(grpc_client_handled_total[5m])) by (grpc_method) > 0

Repository changes fail with a 401 Unauthorized error

If you run Gitaly on its own server and notice these conditions:

• Users can successfully clone and fetch repositories by using both SSH and HTTPS.
• Users can't push to repositories, or receive a 401 Unauthorized message when attempting to make changes to them in the web UI.

Gitaly may be failing to authenticate with the Gitaly client because it has the wrong secrets file.

Confirm the following are all true:

• When any user performs a git push to any repository on this Gitaly server, it fails with a 401 Unauthorized error:

  remote: GitLab: 401 Unauthorized
  To <REMOTE_URL>
  ! [remote rejected] branch-name -> branch-name (pre-receive hook declined)
  error: failed to push some refs to '<REMOTE_URL>'

• When any user adds or modifies a file from the repository using the GitLab UI, it immediately fails with a red 401 Unauthorized banner.

• Creating a new project and initializing it with a README successfully creates the project but doesn't create the README.

• When tailing the logs on a Gitaly client and reproducing the error, you get 401 errors when reaching the /api/v4/internal/allowed endpoint:

  # api_json.log
  {
    "time": "2019-07-18T00:30:14.967Z",
    "severity": "INFO",
    "duration": 0.57,
    "db": 0,
    "view": 0.57,
    "status": 401,
    "method": "POST",
    "path": "\/api\/v4\/internal\/allowed",
    "params": [
      {
        "key": "action",
        "value": "git-receive-pack"
      },
      {
        "key": "changes",
        "value": "REDACTED"
      },
      {
        "key": "gl_repository",
        "value": "REDACTED"
      },
      {
        "key": "project",
        "value": "\/path\/to\/project.git"
      },
      {
        "key": "protocol",
        "value": "web"
      },
      {
        "key": "env",
        "value": "{\"GIT_ALTERNATE_OBJECT_DIRECTORIES\":[],\"GIT_ALTERNATE_OBJECT_DIRECTORIES_RELATIVE\":[],\"GIT_OBJECT_DIRECTORY\":null,\"GIT_OBJECT_DIRECTORY_RELATIVE\":null}"
      },
      {
        "key": "user_id",
        "value": "2"
      },
      {
        "key": "secret_token",
        "value": "[FILTERED]"
      }
    ],
    "host": "gitlab.example.com",
    "ip": "REDACTED",
    "ua": "Ruby",
    "route": "\/api\/:version\/internal\/allowed",
    "queue_duration": 4.24,
    "gitaly_calls": 0,
    "gitaly_duration": 0,
    "correlation_id": "XPUZqTukaP3"
  }
  
  # nginx_access.log
  [IP] - - [18/Jul/2019:00:30:14 +0000] "POST /api/v4/internal/allowed HTTP/1.1" 401 30 "" "Ruby"

To fix this problem, confirm that your gitlab-secrets.json file on the Gitaly server matches the one on Gitaly client. If it doesn't match, update the secrets file on the Gitaly server to match the Gitaly client, then reconfigure.

If you've confirmed that your gitlab-secrets.json file is the same on all Gitaly servers and clients, the application might be fetching this secret from a different file. Your Gitaly server's config.toml file indicates the secrets file in use. If that setting is missing, GitLab defaults to using .gitlab_shell_secret under /opt/gitlab/embedded/service/gitlab-rails/.gitlab_shell_secret.

Repository pushes fail with a deny updating a hidden ref error

Due to a change introduced in GitLab 13.12, Gitaly has read-only, internal GitLab references that users are not permitted to update. If you attempt to update internal references with git push --mirror, Git returns the rejection error, deny updating a hidden ref.

The following references are read-only:

• refs/environments/
• refs/keep-around/
• refs/merge-requests/
• refs/pipelines/

To mirror-push branches and tags only, and avoid attempting to mirror-push protected refs, run:

git push origin +refs/heads/*:refs/heads/* +refs/tags/*:refs/tags/*

Any other namespaces that the administrator wants to push can be included there as well via additional patterns.

Command line tools cannot connect to Gitaly

gRPC cannot reach your Gitaly server if:

• You can't connect to a Gitaly server with command-line tools.
• Certain actions result in a 14: Connect Failed error message.

Verify you can reach Gitaly by using TCP:

sudo gitlab-rake gitlab:tcp_check[GITALY_SERVER_IP,GITALY_LISTEN_PORT]

If the TCP connection:

• Fails, check your network settings and your firewall rules.
• Succeeds, your networking and firewall rules are correct.

If you use proxy servers in your command line environment such as Bash, these can interfere with your gRPC traffic.

If you use Bash or a compatible command line environment, run the following commands to determine whether you have proxy servers configured:

echo $http_proxy
echo $https_proxy

If either of these variables have a value, your Gitaly CLI connections may be getting routed through a proxy which cannot connect to Gitaly.

To remove the proxy setting, run the following commands (depending on which variables had values):

unset http_proxy
unset https_proxy

Permission denied errors appearing in Gitaly or Praefect logs when accessing repositories

You might see the following in Gitaly and Praefect logs:

{
  ...
  "error":"rpc error: code = PermissionDenied desc = permission denied",
  "grpc.code":"PermissionDenied",
  "grpc.meta.client_name":"gitlab-web",
  "grpc.request.fullMethod":"/gitaly.ServerService/ServerInfo",
  "level":"warning",
  "msg":"finished unary call with code PermissionDenied",
  ...
}

This is a GRPC call error response code.

If this error occurs, even though the Gitaly auth tokens are set up correctly, it's likely that the Gitaly servers are experiencing clock drift.

Ensure the Gitaly clients and servers are synchronized, and use an NTP time server to keep them synchronized.

Gitaly not listening on new address after reconfiguring

When updating the gitaly['listen_addr'] or gitaly['prometheus_listen_addr'] values, Gitaly may continue to listen on the old address after a sudo gitlab-ctl reconfigure.

When this occurs, run sudo gitlab-ctl restart to resolve the issue. This should no longer be necessary because this issue is resolved.

Permission denied errors appearing in Gitaly logs when accessing repositories from a standalone Gitaly node

If this error occurs even though file permissions are correct, it's likely that the Gitaly node is experiencing clock drift.

Please ensure that the GitLab and Gitaly nodes are synchronized and use an NTP time server to keep them synchronized if possible.

Health check warnings

The following warning in /var/log/gitlab/praefect/current can be ignored.

"error":"full method name not found: /grpc.health.v1.Health/Check",
"msg":"error when looking up method info"

File not found errors

The following errors in /var/log/gitlab/gitaly/current can be ignored. They are caused by the GitLab Rails application checking for specific files that do not exist in a repository.

"error":"not found: .gitlab/route-map.yml"
"error":"not found: Dockerfile"
"error":"not found: .gitlab-ci.yml"

Git pushes are slow when Dynatrace is enabled

Dynatrace can cause the /opt/gitlab/embedded/bin/gitaly-hooks reference transaction hook, to take several seconds to start up and shut down. gitaly-hooks is executed twice when users push, which causes a significant delay.

If Git pushes are too slow when Dynatrace is enabled, disable Dynatrace.

Troubleshoot Praefect (Gitaly Cluster)

The following sections provide possible solutions to Gitaly Cluster errors.

Check cluster health

Introduced in GitLab 14.5.

The check Praefect sub-command runs a series of checks to determine the health of the Gitaly Cluster.

gitlab-ctl praefect check

The following sections describe the checks that are run.

Praefect migrations

Because Database migrations must be up to date for Praefect to work correctly, checks if Praefect migrations are up to date.

If this check fails:

1. See the schema_migrations table in the database to see which migrations have run.
2. Run praefect sql-migrate to bring the migrations up to date.

Node connectivity and disk access

Checks if Praefect can reach all of its Gitaly nodes, and if each Gitaly node has read and write access to all of its storages.

If this check fails:

1. Confirm the network addresses and tokens are set up correctly:
   • In the Praefect configuration.
   • In each Gitaly node's configuration.
2. On the Gitaly nodes, check that the gitaly process being run as git. There might be a permissions issue that is preventing Gitaly from accessing its storage directories.
3. Confirm that there are no issues with the network that connects Praefect to Gitaly nodes.

Database read and write access

Checks if Praefect can read from and write to the database.

If this check fails:

1. See if the Praefect database is in recovery mode. In recovery mode, tables may be read only. To check, run:

   select pg_is_in_recovery()

2. Confirm that the user that Praefect uses to connect to PostgreSQL has read and write access to the database.

3. See if the database has been placed into read-only mode. To check, run:

   show default_transaction_read_only

Inaccessible repositories

Checks how many repositories are inaccessible because they are missing a primary assignment, or their primary is unavailable.

If this check fails:

1. See if any Gitaly nodes are down. Run praefect ping-nodes to check.
2. Check if there is a high load on the Praefect database. If the Praefect database is slow to respond, it can lead health checks failing to persist to the database, leading Praefect to think nodes are unhealthy.

Check clock synchronization

Introduced in GitLab 14.8.

Authentication between Praefect and the Gitaly servers requires the server times to be in sync so the token check succeeds.

This check helps identify the root cause of permission denied errors being logged by Praefect.

Praefect errors in logs

If you receive an error, check /var/log/gitlab/gitlab-rails/production.log.

Here are common errors and potential causes:

• 500 response code
  • ActionView::Template::Error (7:permission denied)
    • praefect['auth_token'] and gitlab_rails['gitaly_token'] do not match on the GitLab server.
  • Unable to save project. Error: 7:permission denied
    • Secret token in praefect['storage_nodes'] on GitLab server does not match the value in gitaly['auth_token'] on one or more Gitaly servers.
• 503 response code
  • GRPC::Unavailable (14:failed to connect to all addresses)
    • GitLab was unable to reach Praefect.
  • GRPC::Unavailable (14:all SubCons are in TransientFailure...)
    • Praefect cannot reach one or more of its child Gitaly nodes. Try running the Praefect connection checker to diagnose.

Praefect database experiencing high CPU load

Some common reasons for the Praefect database to experience elevated CPU usage include:

• Prometheus metrics scrapes running an expensive query. If you have GitLab 14.2 or above, set praefect['separate_database_metrics'] = true in gitlab.rb.
• Read distribution caching is disabled, increasing the number of queries made to the database when user traffic is high. Ensure read distribution caching is enabled.

Determine primary Gitaly node

To determine the primary node of a repository:

• In GitLab 14.6 and later, use the praefect metadata subcommand.

• In GitLab 13.12 to GitLab 14.5 with repository-specific primaries, use the gitlab:praefect:replicas Rake task.

• With legacy election strategies in GitLab 13.12 and earlier, the primary was the same for all repositories in a virtual storage. To determine the current primary Gitaly node for a specific virtual storage:

  • Use the Shard Primary Election Grafana chart on the Gitlab Omnibus - Praefect dashboard. This is recommended.

  • If you do not have Grafana set up, use the following command on each host of each Praefect node:

    curl localhost:9652/metrics | grep gitaly_praefect_primaries`

View repository metadata

Introduced in GitLab 14.6.

Gitaly Cluster maintains a metadata database about the repositories stored on the cluster. Use the praefect metadata subcommand to inspect the metadata for troubleshooting.

You can retrieve a repository's metadata by its Praefect-assigned repository ID:

sudo /opt/gitlab/embedded/bin/praefect -config /var/opt/gitlab/praefect/config.toml metadata -repository-id <repository-id>

You can also retrieve a repository's metadata by its virtual storage and relative path:

sudo /opt/gitlab/embedded/bin/praefect -config /var/opt/gitlab/praefect/config.toml metadata -virtual-storage <virtual-storage> -relative-path <relative-path>

Examples

To retrieve the metadata for a repository with a Praefect-assigned repository ID of 1:

sudo /opt/gitlab/embedded/bin/praefect -config /var/opt/gitlab/praefect/config.toml metadata -repository-id 1

To retrieve the metadata for a repository with virtual storage default and relative path @hashed/b1/7e/b17ef6d19c7a5b1ee83b907c595526dcb1eb06db8227d650d5dda0a9f4ce8cd9.git:

sudo /opt/gitlab/embedded/bin/praefect -config /var/opt/gitlab/praefect/config.toml metadata -virtual-storage default -relative-path @hashed/b1/7e/b17ef6d19c7a5b1ee83b907c595526dcb1eb06db8227d650d5dda0a9f4ce8cd9.git

Either of these examples retrieve the following metadata for an example repository:

Repository ID: 54771
Virtual Storage: "default"
Relative Path: "@hashed/b1/7e/b17ef6d19c7a5b1ee83b907c595526dcb1eb06db8227d650d5dda0a9f4ce8cd9.git"
Replica Path: "@hashed/b1/7e/b17ef6d19c7a5b1ee83b907c595526dcb1eb06db8227d650d5dda0a9f4ce8cd9.git"
Primary: "gitaly-1"
Generation: 1
Replicas:
- Storage: "gitaly-1"
  Assigned: true
  Generation: 1, fully up to date
  Healthy: true
  Valid Primary: true
  Verified At: 2021-04-01 10:04:20 +0000 UTC
- Storage: "gitaly-2"
  Assigned: true
  Generation: 0, behind by 1 changes
  Healthy: true
  Valid Primary: false
  Verified At: unverified
- Storage: "gitaly-3"
  Assigned: true
  Generation: replica not yet created
  Healthy: false
  Valid Primary: false
  Verified At: unverified

Available metadata

The metadata retrieved by praefect metadata includes the fields in the following tables.

For each replica, the following metadata is available:

Check that repositories are in sync

Is some cases the Praefect database can get out of sync with the underlying Gitaly nodes. To check that a given repository is fully synced on all nodes, run the gitlab:praefect:replicas Rake task that checksums the repository on all Gitaly nodes.

The Praefect dataloss command only checks the state of the repository in the Praefect database, and cannot be relied to detect sync problems in this scenario.

Relation does not exist errors

By default Praefect database tables are created automatically by gitlab-ctl reconfigure task.

However, the Praefect database tables are not created on initial reconfigure and can throw errors that relations do not exist if either:

• The gitlab-ctl reconfigure command isn't executed.
• There are errors during the execution.

For example:

• ERROR: relation "node_status" does not exist at character 13

• ERROR: relation "replication_queue_lock" does not exist at character 40

• This error:

  {"level":"error","msg":"Error updating node: pq: relation \"node_status\" does not exist","pid":210882,"praefectName":"gitlab1x4m:0.0.0.0:2305","time":"2021-04-01T19:26:19.473Z","virtual_storage":"praefect-cluster-1"}

To solve this, the database schema migration can be done using sql-migrate sub-command of the praefect command:

$ sudo /opt/gitlab/embedded/bin/praefect -config /var/opt/gitlab/praefect/config.toml sql-migrate
praefect sql-migrate: OK (applied 21 migrations)

Requests fail with 'repository scoped: invalid Repository' errors

This indicates that the virtual storage name used in the Praefect configuration does not match the storage name used in git_data_dirs setting for GitLab.

Resolve this by matching the virtual storage names used in Praefect and GitLab configuration.

Gitaly Cluster performance issues on cloud platforms

Praefect does not require a lot of CPU or memory, and can run on small virtual machines. Cloud services may place other limits on the resources that small VMs can use, such as disk IO and network traffic.

Praefect nodes generate a lot of network traffic. The following symptoms can be observed if their network bandwidth has been throttled by the cloud service:

• Poor performance of Git operations.
• High network latency.
• High memory use by Praefect.

Possible solutions:

• Provision larger VMs to gain access to larger network traffic allowances.
• Use your cloud service's monitoring and logging to check that the Praefect nodes are not exhausting their traffic allowances.

Profiling Gitaly

Gitaly exposes several of Golang's built-in performance profiling tools on the Prometheus listen port. For example, if Prometheus is listening on port 9236 of the GitLab server:

• Get a list of running goroutines and their backtraces:

  curl --output goroutines.txt "http://<gitaly_server>:9236/debug/pprof/goroutine?debug=2"

• Run a CPU profile for 30 seconds:

  curl --output cpu.bin "http://<gitaly_server>:9236/debug/pprof/profile"

• Profile heap memory usage:

  curl --output heap.bin "http://<gitaly_server>:9236/debug/pprof/heap"

• Record a 5 second execution trace. This will impact Gitaly's performance while running:

  curl --output trace.bin "http://<gitaly_server>:9236/debug/pprof/trace?seconds=5"

On a host with go installed, the CPU profile and heap profile can be viewed in a browser:

go tool pprof -http=:8001 cpu.bin
go tool pprof -http=:8001 heap.bin

Execution traces can be viewed by running:

go tool trace heap.bin