Certain pushes fail on 11.2.0 and 11.2.1, work on 11.1.4

Summary

Certain commits fail to push to self-hosted GitLab on versions 11.2.0 and 11.2.1.

Steps to reproduce

I was unable to fully determine what triggers the error. While pushing most commits to the repository worked, some failed:

Pushing to git@censored:apps/censored/censored-web.git
Counting objects: 920, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (839/839), done.
Writing objects: 100% (920/920), 4.55 MiB | 1.18 MiB/s, done.
Total 920 (delta 61), reused 889 (delta 58)
remote: Resolving deltas: 100% (61/61), completed with 1 local object.
remote: GitLab: API is not accessible
To censored:apps/censored/censored-web.git
 ! [remote rejected]   master → master (pre-receive hook declined)
error: failed to push some refs to 'git@censored:apps/censored/censored-web.git'

I completely followed the upgrade steps and verified that the official docker image properly updated gitaly config.toml.

I've verified that the repository does not use LFS, it's disabled for the entire group and there is no LFS in any .gitattributes in the repository.

Very relevant logs

Omnibus logs 
==> /var/log/gitlab/gitaly/current <==
2018-08-23_09:33:40.06744 time="2018-08-23T09:33:40Z" level=info msg="finished streaming call" error="rpc error: code = Canceled desc = rpc error: code = Canceled desc = context canceled" grpc.code=Canceled grpc.meta.client_name=gitlab-web grpc.method=GetNewLFSPointers grpc.request.glRepository=project-67 grpc.request.repoPath=apps/censored/censored-web.git grpc.request.repoStorage=default grpc.request.topLevelGroup=apps grpc.service=gitaly.BlobService grpc.time_ms=30000 peer.address=@ span.kind=server system=grpc

==> /var/log/gitlab/gitlab-rails/production.log <==


GRPC::DeadlineExceeded (4:Deadline Exceeded):
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grpc-1.11.0-x86_64-linux/src/ruby/lib/grpc/generic/active_call.rb:31:in check_status' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grpc-1.11.0-x86_64-linux/src/ruby/lib/grpc/generic/active_call.rb:180:in attach_status_results_and_complete_call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grpc-1.11.0-x86_64-linux/src/ruby/lib/grpc/generic/active_call.rb:169:in receive_and_check_status' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grpc-1.11.0-x86_64-linux/src/ruby/lib/grpc/generic/active_call.rb:328:in block in each_remote_read_then_finish'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grpc-1.11.0-x86_64-linux/src/ruby/lib/grpc/generic/active_call.rb:325:in loop' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grpc-1.11.0-x86_64-linux/src/ruby/lib/grpc/generic/active_call.rb:325:in each_remote_read_then_finish'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/gitaly_client/blob_service.rb:107:in each' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/gitaly_client/blob_service.rb:107:in flat_map'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/gitaly_client/blob_service.rb:107:in map_lfs_pointers' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/gitaly_client/blob_service.rb:90:in get_new_lfs_pointers'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/git/lfs_changes.rb:10:in new_pointers' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/checks/lfs_integrity.rb:13:in objects_missing?'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/instrumentation.rb:159:in block in objects_missing?' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/method_call.rb:34:in measure'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/instrumentation.rb:159:in objects_missing?' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/checks/change_access.rb:199:in lfs_objects_exist_check'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/instrumentation.rb:159:in block in lfs_objects_exist_check' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/method_call.rb:34:in measure'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/instrumentation.rb:159:in lfs_objects_exist_check' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/checks/change_access.rb:43:in exec'
/opt/gitlab/embedded/service/gitlab-rails/ee/lib/ee/gitlab/checks/change_access.rb:20:in exec' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/git_access.rb:292:in check_single_change_access'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/instrumentation.rb:159:in block in check_single_change_access' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/method_call.rb:34:in measure'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/instrumentation.rb:159:in check_single_change_access' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/git_access.rb:272:in block in check_change_access!'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/git_access.rb:267:in each' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/git_access.rb:267:in with_index'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/git_access.rb:267:in check_change_access!' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/instrumentation.rb:159:in block in check_change_access!'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/method_call.rb:34:in measure' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/instrumentation.rb:159:in check_change_access!'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/git_access.rb:255:in check_push_access!' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/instrumentation.rb:159:in block in check_push_access!'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/method_call.rb:34:in measure' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/instrumentation.rb:159:in check_push_access!'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/git_access.rb:68:in check' /opt/gitlab/embedded/service/gitlab-rails/ee/lib/ee/gitlab/git_access.rb:11:in check'
/opt/gitlab/embedded/service/gitlab-rails/lib/api/internal.rb:53:in block (2 levels) in <class:Internal>' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/endpoint.rb:57:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/endpoint.rb:57:in block (2 levels) in generate_api_method' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/activesupport-4.2.10/lib/active_support/notifications.rb:166:in instrument'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/endpoint.rb:56:in block in generate_api_method' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/endpoint.rb:262:in block in run'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/activesupport-4.2.10/lib/active_support/notifications.rb:166:in instrument' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/endpoint.rb:243:in run'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/endpoint.rb:313:in block in build_stack' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/middleware/base.rb:31:in call!'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/middleware/base.rb:24:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/middleware/base.rb:31:in call!'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/middleware/base.rb:24:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-oauth2-1.2.3/lib/rack/oauth2/server/resource.rb:20:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-oauth2-1.2.3/lib/rack/oauth2/server/resource/bearer.rb:8:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/middleware/error.rb:37:in block in call!'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/middleware/error.rb:36:in catch' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/middleware/error.rb:36:in call!'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/middleware/base.rb:24:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape_logging-1.7.0/lib/grape_logging/middleware/request_logger.rb:60:in block in call!'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape_logging-1.7.0/lib/grape_logging/middleware/request_logger.rb:58:in catch' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape_logging-1.7.0/lib/grape_logging/middleware/request_logger.rb:58:in call!'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/middleware/base.rb:24:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/head.rb:13:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/endpoint.rb:227:in call!' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/endpoint.rb:221:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/router/route.rb:72:in exec' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/router.rb:121:in process_route'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/router.rb:74:in block in identity' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/router.rb:93:in transaction'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/router.rb:72:in identity' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/router.rb:57:in block in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/router.rb:137:in with_optimization' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/router.rb:56:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/api.rb:119:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/api.rb:45:in call!'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/grape-1.0.3/lib/grape/api.rb:40:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/routing/mapper.rb:51:in serve'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/journey/router.rb:43:in block in serve' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/journey/router.rb:30:in each'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/journey/router.rb:30:in serve' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/routing/route_set.rb:817:in call'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/multipart.rb:97:in call' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/request_profiler/middleware.rb:14:in call'
/opt/gitlab/embedded/service/gitlab-rails/ee/lib/gitlab/jira/middleware.rb:15:in call' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/go.rb:17:in call'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/etag_caching/middleware.rb:11:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/batch-loader-1.2.1/lib/batch_loader/middleware.rb:11:in call'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/rails_queue_duration.rb:22:in call' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/rack_middleware.rb:15:in block in call'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/transaction.rb:53:in run' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/rack_middleware.rb:15:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-attack-4.4.1/lib/rack/attack.rb:107:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/warden-1.2.7/lib/warden/manager.rb:36:in block in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/warden-1.2.7/lib/warden/manager.rb:35:in catch' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/warden-1.2.7/lib/warden/manager.rb:35:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-cors-1.0.2/lib/rack/cors.rb:97:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/etag.rb:24:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/conditionalget.rb:38:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/head.rb:13:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/middleware/params_parser.rb:27:in call' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/read_only/controller.rb:40:in call'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/read_only.rb:16:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/middleware/flash.rb:260:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/session/abstract/id.rb:225:in context' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/session/abstract/id.rb:220:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/middleware/cookies.rb:560:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/activerecord-4.2.10/lib/active_record/query_cache.rb:36:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract/connection_pool.rb:653:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/middleware/callbacks.rb:29:in block in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/activesupport-4.2.10/lib/active_support/callbacks.rb:88:in __run_callbacks__' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/activesupport-4.2.10/lib/active_support/callbacks.rb:778:in _run_call_callbacks'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/activesupport-4.2.10/lib/active_support/callbacks.rb:81:in run_callbacks' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/middleware/callbacks.rb:27:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/middleware/remote_ip.rb:78:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/middleware/debug_exceptions.rb:17:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/middleware/show_exceptions.rb:30:in call' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/basic_health_check.rb:25:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/railties-4.2.10/lib/rails/rack/logger.rb:38:in call_app' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/railties-4.2.10/lib/rails/rack/logger.rb:20:in block in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/activesupport-4.2.10/lib/active_support/tagged_logging.rb:68:in block in tagged' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/activesupport-4.2.10/lib/active_support/tagged_logging.rb:26:in tagged'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/activesupport-4.2.10/lib/active_support/tagged_logging.rb:68:in tagged' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/railties-4.2.10/lib/rails/rack/logger.rb:20:in call'
/opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/request_context.rb:18:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/request_store-1.3.1/lib/request_store/middleware.rb:9:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/actionpack-4.2.10/lib/action_dispatch/middleware/request_id.rb:21:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/methodoverride.rb:22:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/runtime.rb:18:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/lock.rb:17:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/sendfile.rb:113:in call' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/requests_rack_middleware.rb:27:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/sentry-raven-2.7.2/lib/raven/integrations/rack.rb:51:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/railties-4.2.10/lib/rails/engine.rb:518:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/railties-4.2.10/lib/rails/application.rb:165:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/railties-4.2.10/lib/rails/railtie.rb:194:in public_send'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/railties-4.2.10/lib/rails/railtie.rb:194:in method_missing' /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/release_env.rb:10:in call'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/urlmap.rb:66:in block in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/urlmap.rb:50:in each'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/rack-1.6.10/lib/rack/urlmap.rb:50:in call' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/unicorn-5.1.0/lib/unicorn/http_server.rb:562:in process_client'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/unicorn-worker-killer-0.4.4/lib/unicorn/worker_killer.rb:52:in process_client' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/unicorn-5.1.0/lib/unicorn/http_server.rb:658:in worker_loop'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/unicorn-5.1.0/lib/unicorn/http_server.rb:508:in spawn_missing_workers' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/unicorn-5.1.0/lib/unicorn/http_server.rb:132:in start'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/unicorn-5.1.0/bin/unicorn:126:in <top (required)>' /opt/gitlab/embedded/bin/unicorn:23:in load'
/opt/gitlab/embedded/bin/unicorn:23:in <top (required)>' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/lib/bundler/cli/exec.rb:74:in load'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/lib/bundler/cli/exec.rb:74:in kernel_load' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/lib/bundler/cli/exec.rb:28:in run'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/lib/bundler/cli.rb:424:in exec' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/lib/bundler/vendor/thor/lib/thor/command.rb:27:in run'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/lib/bundler/vendor/thor/lib/thor/invocation.rb:126:in invoke_command' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/lib/bundler/vendor/thor/lib/thor.rb:387:in dispatch'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/lib/bundler/cli.rb:27:in dispatch' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/lib/bundler/vendor/thor/lib/thor/base.rb:466:in start'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/lib/bundler/cli.rb:18:in start' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/exe/bundle:30:in block in <top (required)>'
/opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/lib/bundler/friendly_errors.rb:124:in with_friendly_errors' /opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/bundler-1.16.2/exe/bundle:22:in <top (required)>'
/opt/gitlab/embedded/bin/bundle:23:in load' /opt/gitlab/embedded/bin/bundle:23:in '


==> /var/log/gitlab/gitlab-rails/api_json.log <==
{"time":"2018-08-23T09:33:40.068Z","severity":"INFO","duration":30083.52,"db":25.98,"view":30057.54,"status":500,"method":"POST","path":"/api/v4/internal/allowed","params":{"action":"git-receive-pack","changes":"2e491d375698dd7d78c35b6d9b743dffa82b702f 52afb702b2ecdf2acb266ae9a6f41be8536935d3 refs/heads/master\n","gl_repository":"project-67","project":"/data/gitlab-data/git-data/repositories/apps/censored/censored-web.git","protocol":"ssh","env":"{"GIT_ALTERNATE_OBJECT_DIRECTORIES":["/data/gitlab-data/git-data/repositories/apps/censored/censored-web.git/./objects"],"GIT_ALTERNATE_OBJECT_DIRECTORIES_RELATIVE":["objects"],"GIT_OBJECT_DIRECTORY":"/data/gitlab-data/git-data/repositories/apps/censored/censored-web.git/./objects/incoming-lKu7Us","GIT_OBJECT_DIRECTORY_RELATIVE":"objects/incoming-lKu7Us"}","key_id":"[FILTERED]","secret_token":"[FILTERED]"},"host":"127.0.0.1","ip":"127.0.0.1","ua":"Ruby"}


==> /var/log/gitlab/gitlab-shell/gitlab-shell.log <==
time="2018-08-23T09:33:40+00:00" level=info msg="finished HTTP request" duration=30.146258141 method=POST pid=3907 url="http://127.0.0.1:8080/api/v4/internal/allowed"
time="2018-08-23T09:33:40+00:00" level=error msg="Call failed" body="{"message":"500 Internal Server Error"}" code=500 method=POST pid=3907 url="http://127.0.0.1:8080/api/v4/internal/allowed"


==> /var/log/gitlab/gitaly/current <==
2018-08-23_09:33:40.16023 time="2018-08-23T09:33:40Z" level=info msg="finished streaming call" grpc.code=OK grpc.method=SSHReceivePack grpc.request.glRepository=project-67 grpc.request.repoPath=apps/censored/censored-web.git grpc.request.repoStorage=default grpc.request.topLevelGroup=apps grpc.service=gitaly.SSHService grpc.time_ms=36515 peer.address=@ span.kind=server system=grpc


==> /var/log/gitlab/sshd/current <==
2018-08-23_09:33:40.17505 Received disconnect from 193.86.64.162 port 52035:11: disconnected by user
2018-08-23_09:33:40.17507 Disconnected from 193.86.64.162 port 52035

Output of checks

Self hosted omnibus from dockerhub, 11.2.1-ee.0.

Results of GitLab environment info

Expand for output related to GitLab environment info 
System information
System:
Proxy:		no
Current User:	git
Using RVM:	no
Ruby Version:	2.4.4p296
Gem Version:	2.7.6
Bundler Version:1.16.2
Rake Version:	12.3.1
Redis Version:	3.2.11
Git Version:	2.18.0
Sidekiq Version:5.1.3
Go Version:	unknown

GitLab information
Version:	11.2.1-ee
Revision:	df8846c
Directory:	/opt/gitlab/embedded/service/gitlab-rails
DB Adapter:	postgresql
DB Version:	9.6.8
URL:		https://mangoweb.org
HTTP Clone URL:	https://mangoweb.org/some-group/some-project.git
SSH Clone URL:	git@mangoweb.org:some-group/some-project.git
Elasticsearch:	no
Geo:		no
Using LDAP:	no
Using Omniauth:	no


GitLab Shell
Version:	8.1.1
Repository storage paths:
  • default: /data/gitlab-data/git-data/repositories Hooks: /opt/gitlab/embedded/service/gitlab-shell/hooks Git: /opt/gitlab/embedded/bin/git

Results of GitLab application Check

Expand for output related to the GitLab application check 
Check GitLab API access: OK
Redis available via internal API: OK

Access to /data/gitlab-data/home/.ssh/authorized_keys: OK
gitlab-shell self-check successful


Checking GitLab Shell ... Finished


Checking Sidekiq ...


Running? ... yes
Number of Sidekiq processes ... 1


Checking Sidekiq ... Finished


Reply by email is disabled in config/gitlab.yml
Checking LDAP ...


LDAP is disabled in config/gitlab.yml


Checking LDAP ... Finished


Checking GitLab ...


Git configured correctly? ... yes
Database config exists? ... yes
All migrations up? ... yes
Database contains orphaned GroupMembers? ... no
GitLab config exists? ... yes
GitLab config up to date? ... yes
Log directory writable? ... yes
Tmp directory writable? ... yes
Uploads directory exists? ... yes
Uploads directory has correct permissions? ... yes
Uploads directory tmp has correct permissions? ... yes
Init script exists? ... skipped (omnibus-gitlab has no init script)
Init script up-to-date? ... skipped (omnibus-gitlab has no init script)
Projects have namespace: ...


... all yes
.../444 ... yes


Redis version >= 2.8.0? ... yes
Ruby version >= 2.3.5 ? ... yes (2.4.4)
Git version >= 2.9.5 ? ... yes (2.18.0)
Git user has default SSH configuration? ... yes
Active users: ... 39
Elasticsearch version 5.1 - 5.5? ... skipped (elasticsearch is disabled)


Checking GitLab ... Finished
Edited by Mikuláš Dítě