[10.4.5 -> 10.5.0] migration failed

Summary

Migrating the mysql database from 10.4.5 to 10.5.0 failed. Suggestions posted here already applied, won't help.

Relevant logs and/or screenshots

== 20180116193854 CreateLfsFileLocks: migrating ===============================
-- create_table(:lfs_file_locks)
   -> 0.3866s
-- add_index(:lfs_file_locks, [:project_id, :path], {:unique=>true})
rake aborted!
StandardError: An error has occurred, all later migrations canceled:

Mysql2::Error: Index column size too large. The maximum column size is 767 bytes.: CREATE UNIQUE INDEX `index_lfs_file_locks_on_project_id_and_path`  ON `lfs_file_locks` (`project_id`, `path`) 
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:120:in `_query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:120:in `block in query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:119:in `handle_interrupt'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:119:in `query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in `query_with_timing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:317:in `block in execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_adapter.rb:484:in `block in log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_adapter.rb:478:in `log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:317:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/mysql2_adapter.rb:217:in `execute'
/home/git/gitlab/config/initializers/connection_fix.rb:20:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:549:in `add_index'
/home/git/gitlab/config/initializers/mysql_ignore_postgresql_options.rb:23:in `add_index'
/home/git/gitlab/config/initializers/mysql_set_length_for_binary_indexes.rb:15:in `add_index'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:665:in `block in method_missing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:634:in `block in say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:634:in `say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:654:in `method_missing'
/home/git/gitlab/db/migrate/20180116193854_create_lfs_file_locks.rb:16:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:611:in `exec_migration'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:592:in `block (2 levels) in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:591:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract/connection_pool.rb:292:in `with_connection'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:590:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:768:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:1023:in `block in execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:1071:in `ddl_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:1022:in `execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:984:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:980:in `each'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:980:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:823:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:801:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/tasks/database_tasks.rb:139:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/railties/databases.rake:44:in `block (2 levels) in <top (required)>'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/rake-12.3.0/exe/rake:27:in `<top (required)>'

Caused by:
ActiveRecord::StatementInvalid: Mysql2::Error: Index column size too large. The maximum column size is 767 bytes.: CREATE UNIQUE INDEX `index_lfs_file_locks_on_project_id_and_path`  ON `lfs_file_locks` (`project_id`, `path`) 
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:120:in `_query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:120:in `block in query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:119:in `handle_interrupt'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:119:in `query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in `query_with_timing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:317:in `block in execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_adapter.rb:484:in `block in log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_adapter.rb:478:in `log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:317:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/mysql2_adapter.rb:217:in `execute'
/home/git/gitlab/config/initializers/connection_fix.rb:20:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:549:in `add_index'
/home/git/gitlab/config/initializers/mysql_ignore_postgresql_options.rb:23:in `add_index'
/home/git/gitlab/config/initializers/mysql_set_length_for_binary_indexes.rb:15:in `add_index'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:665:in `block in method_missing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:634:in `block in say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:634:in `say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:654:in `method_missing'
/home/git/gitlab/db/migrate/20180116193854_create_lfs_file_locks.rb:16:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:611:in `exec_migration'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:592:in `block (2 levels) in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:591:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract/connection_pool.rb:292:in `with_connection'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:590:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:768:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:1023:in `block in execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:1071:in `ddl_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:1022:in `execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:984:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:980:in `each'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:980:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:823:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:801:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/tasks/database_tasks.rb:139:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/railties/databases.rake:44:in `block (2 levels) in <top (required)>'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/rake-12.3.0/exe/rake:27:in `<top (required)>'

Caused by:
Mysql2::Error: Index column size too large. The maximum column size is 767 bytes.
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:120:in `_query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:120:in `block in query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:119:in `handle_interrupt'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/mysql2-0.4.10/lib/mysql2/client.rb:119:in `query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in `query_with_timing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:317:in `block in execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_adapter.rb:484:in `block in log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_adapter.rb:478:in `log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:317:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/mysql2_adapter.rb:217:in `execute'
/home/git/gitlab/config/initializers/connection_fix.rb:20:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:549:in `add_index'
/home/git/gitlab/config/initializers/mysql_ignore_postgresql_options.rb:23:in `add_index'
/home/git/gitlab/config/initializers/mysql_set_length_for_binary_indexes.rb:15:in `add_index'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:665:in `block in method_missing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:634:in `block in say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:634:in `say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:654:in `method_missing'
/home/git/gitlab/db/migrate/20180116193854_create_lfs_file_locks.rb:16:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:611:in `exec_migration'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:592:in `block (2 levels) in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:591:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/connection_adapters/abstract/connection_pool.rb:292:in `with_connection'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:590:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:768:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:1023:in `block in execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:1071:in `ddl_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:1022:in `execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:984:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:980:in `each'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:980:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:823:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/migration.rb:801:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/tasks/database_tasks.rb:139:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/railties/databases.rake:44:in `block (2 levels) in <top (required)>'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/rake-12.3.0/exe/rake:27:in `<top (required)>'
Tasks: TOP => db:migrate
(See full trace by running task with --trace)

Output of checks

(If you are reporting a bug on GitLab.com, write: This bug happens on GitLab.com)

Results of GitLab environment info

Expand for output related to GitLab environment info 
System information
System:		
Current User:	git
Using RVM:	no
Ruby Version:	2.3.6p384
Gem Version:	2.5.2.2
Bundler Version:1.16.1
Rake Version:	12.3.0
Redis Version:	4.0.8
Git Version:	2.16.2
Sidekiq Version:5.0.5
Go Version:	go1.10 linux/arm

GitLab information
Version:	10.5.0
Revision:	34d57661342
Directory:	/home/git/gitlab
DB Adapter:	mysql2
URL:		https://gitlab.sytes.net
HTTP Clone URL:	https://gitlab.sytes.net/some-group/some-project.git
SSH Clone URL:	ssh://git@gitlab.sytes.net:2222/some-group/some-project.git
Using LDAP:	no
Using Omniauth:	no


GitLab Shell
Version:	5.11.0
Repository storage paths:
  • default: /home/git/repositories Hooks: /home/git/gitlab-shell/hooks Git: /usr/bin/git

Results of GitLab application Check

Expand for output related to the GitLab application check 
Checking GitLab Shell ...

GitLab Shell version >= 6.0.3 ? ... FAIL. Please update gitlab-shell to 6.0.3 from 5.11.0
Repo base directory exists?
default... yes
Repo storage directories are symlinks?
default... no
Repo paths owned by git:root, or git:git?
default... yes
Repo paths access is drwxrws---?
default... yes
hooks directories in repos are links: ...
3/1 ... rake aborted!
GRPC::Unavailable: 14:Connect Failed
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/grpc-1.8.3/src/ruby/lib/grpc/generic/active_call.rb:31:in check_status' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/grpc-1.8.3/src/ruby/lib/grpc/generic/active_call.rb:180:in attach_status_results_and_complete_call'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/grpc-1.8.3/src/ruby/lib/grpc/generic/active_call.rb:372:in request_response' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/grpc-1.8.3/src/ruby/lib/grpc/generic/client_stub.rb:178:in block in request_response'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/grpc-1.8.3/src/ruby/lib/grpc/generic/interceptors.rb:170:in intercept!' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/grpc-1.8.3/src/ruby/lib/grpc/generic/client_stub.rb:177:in request_response'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/grpc-1.8.3/src/ruby/lib/grpc/generic/service.rb:170:in block (3 levels) in rpc_stub_class' /home/git/gitlab/lib/gitlab/gitaly_client.rb:127:in call'
/home/git/gitlab/lib/gitlab/gitaly_client/repository_service.rb:17:in exists?' /home/git/gitlab/lib/gitlab/git/repository.rb:142:in block in exists?'
/home/git/gitlab/lib/gitlab/gitaly_client.rb:232:in block (2 levels) in migrate' /home/git/gitlab/lib/gitlab/gitaly_client.rb:270:in allow_n_plus_1_calls'
/home/git/gitlab/lib/gitlab/gitaly_client.rb:227:in block in migrate' /home/git/gitlab/lib/gitlab/metrics/influx_db.rb:98:in measure'
/home/git/gitlab/lib/gitlab/gitaly_client.rb:225:in migrate' /home/git/gitlab/lib/gitlab/git/repository.rb:140:in exists?'
/home/git/gitlab/app/models/repository.rb:508:in exists?' /home/git/gitlab/app/models/repository.rb:71:in block (2 levels) in cache_method'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:299:in block in fetch' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:585:in block in save_block_result_to_cache'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:547:in block in instrument' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/notifications.rb:166:in instrument'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:547:in instrument' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:584:in save_block_result_to_cache'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:299:in fetch' /home/git/gitlab/lib/repository_cache.rb:20:in fetch'
/home/git/gitlab/app/models/repository.rb:961:in cache_method_output' /home/git/gitlab/app/models/repository.rb:70:in block in cache_method'
/home/git/gitlab/app/models/repository.rb:513:in empty?' /home/git/gitlab/app/models/repository.rb:71:in block (2 levels) in cache_method'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:299:in block in fetch' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:585:in block in save_block_result_to_cache'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:547:in block in instrument' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/notifications.rb:166:in instrument'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:547:in instrument' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:584:in save_block_result_to_cache'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.10/lib/active_support/cache.rb:299:in fetch' /home/git/gitlab/lib/repository_cache.rb:20:in fetch'
/home/git/gitlab/app/models/repository.rb:961:in cache_method_output' /home/git/gitlab/app/models/repository.rb:70:in block in cache_method'
/home/git/gitlab/app/models/project.rb:500:in empty_repo?' /home/git/gitlab/lib/tasks/gitlab/check.rake:186:in block in check_repos_hooks_directory_is_link'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/relation/batches.rb:51:in block (2 levels) in find_each' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/relation/batches.rb:51:in each'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/relation/batches.rb:51:in block in find_each' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/relation/batches.rb:124:in find_in_batches'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/relation/batches.rb:50:in find_each' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.10/lib/active_record/querying.rb:9:in find_each'
/home/git/gitlab/lib/tasks/gitlab/check.rake:182:in check_repos_hooks_directory_is_link' /home/git/gitlab/lib/tasks/gitlab/check.rake:51:in block (3 levels) in <top (required)>'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/rake-12.3.0/exe/rake:27:in `<top (required)>'
Tasks: TOP => gitlab:check => gitlab:gitlab_shell:check
(See full trace by running task with --trace)

Possible fixes

reexecuting the migration fails, as the index of the table already exists. Got rid of this by removing the table with:

DROP TABLE lfs_file_locks;