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7.5.3 to 7.6.3 Upgrade : MySQL migration error

Following the issue #924 (closed), I open a new as I do not have the same issue as @chadima.jiri states.

Here is what I said:

--- BEGIN ---

I Tried to update this morning using the upgrader script and going through the 7.5 to 7.6 update method both have the same error on migration.

$ sudo -u git -H bundle exec rake db:migrate RAILS_ENV=production
== 20141121161704 AddIdentityTable: migrating =================================
-- create_table(:identities)
rake aborted!
StandardError: An error has occurred, all later migrations canceled:

Mysql2::Error: Table 'identities' already exists: CREATE TABLE `identities` (`id` int(11) auto_increment PRIMARY KEY, `extern_uid` varchar(255), `provider` varchar(255), `user_id` int(11)) ENGINE=InnoDB/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:301:in `query'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:301:in `block in execute'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_adapter.rb:373:in `block in log'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activesupport-4.1.1/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_adapter.rb:367:in `log'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:301:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/mysql2_adapter.rb:228:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract/schema_statements.rb:205:in `create_table'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:458:in `create_table'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:649:in `block in method_missing'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:621:in `block in say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:621:in `say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:641:in `method_missing'
/home/git/gitlab/db/migrate/20141121161704_add_identity_table.rb:3:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:598:in `exec_migration'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:579:in `block (2 levels) in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:578:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract/connection_pool.rb:294:in `with_connection'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:577:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:752:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:992:in `block in execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:1040:in `ddl_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:991:in `execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:953:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:949:in `each'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:949:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:807:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:785:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/railties/databases.rake:34:in `block (2 levels) in <top (required)>'
ActiveRecord::StatementInvalid: Mysql2::Error: Table 'identities' already exists: CREATE TABLE `identities` (`id` int(11) auto_increment PRIMARY KEY, `extern_uid` varchar(255), `provider` varchar(255), `user_id` int(11)) ENGINE=InnoDB
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:301:in `query'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:301:in `block in execute'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_adapter.rb:373:in `block in log'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activesupport-4.1.1/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_adapter.rb:367:in `log'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:301:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/mysql2_adapter.rb:228:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract/schema_statements.rb:205:in `create_table'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:458:in `create_table'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:649:in `block in method_missing'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:621:in `block in say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:621:in `say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:641:in `method_missing'
/home/git/gitlab/db/migrate/20141121161704_add_identity_table.rb:3:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:598:in `exec_migration'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:579:in `block (2 levels) in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:578:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract/connection_pool.rb:294:in `with_connection'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:577:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:752:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:992:in `block in execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:1040:in `ddl_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:991:in `execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:953:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:949:in `each'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:949:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:807:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:785:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/railties/databases.rake:34:in `block (2 levels) in <top (required)>'
Mysql2::Error: Table 'identities' already exists
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:301:in `query'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:301:in `block in execute'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_adapter.rb:373:in `block in log'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activesupport-4.1.1/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_adapter.rb:367:in `log'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:301:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/mysql2_adapter.rb:228:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract/schema_statements.rb:205:in `create_table'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:458:in `create_table'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:649:in `block in method_missing'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:621:in `block in say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:621:in `say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:641:in `method_missing'
/home/git/gitlab/db/migrate/20141121161704_add_identity_table.rb:3:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:598:in `exec_migration'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:579:in `block (2 levels) in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:578:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/connection_adapters/abstract/connection_pool.rb:294:in `with_connection'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:577:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:752:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:992:in `block in execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:1040:in `ddl_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:991:in `execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:953:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:949:in `each'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:949:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:807:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/migration.rb:785:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/activerecord-4.1.1/lib/active_record/railties/databases.rake:34:in `block (2 levels) in <top (required)>'
Tasks: TOP => db:migrate
(See full trace by running task with --trace)

Now I revert from snapshots with VMWare so any restart is from a fully working 7.5.3 version.

Thanks for your help.

--- END ---

Further information on my installation:

Checking Environment ...

Git configured for git user? ... yes

Checking Environment ... Finished

Checking GitLab Shell ...

GitLab Shell version >= 2.2.0 ? ... OK (2.2.0)
Repo base directory exists? ... yes
Repo base directory is a symlink? ... no
Repo base owned by git:git? ... yes
Repo base access is drwxrws---? ... yes
Satellites access is drwxr-x---? ... yes
hooks directories in repos are links: ... 
[snip]
USER / PROJECT ... ok
[/snip]
Running /home/git/gitlab-shell/bin/check
Check GitLab API access: OK
Check directories and files: 
	/home/git/repositories: OK
	/home/git/.ssh/authorized_keys: OK
Test redis-cli executable: redis-cli 2.4.14
Send ping to redis server: PONG
gitlab-shell self-check successful

Checking GitLab Shell ... Finished

Checking Sidekiq ...

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

Checking Sidekiq ... Finished

Checking LDAP ...

LDAP users with access to your GitLab server (only showing the first 100 results)
Server: ldap
 
[snip]
	DN: uid=USERUID,ou=people,dc=DC,dc=fr	 supannAliasLogin: USER
[/snip]

Checking LDAP ... Finished

Checking GitLab ...

Database config exists? ... yes
Database is SQLite ... no
All migrations up? ... yes
Database contains orphaned GroupMembers? ... no
GitLab config exists? ... yes
GitLab config outdated? ... no
Log directory writable? ... yes
Tmp directory writable? ... yes
Init script exists? ... yes
Init script up-to-date? ... yes
projects have namespace: ... 
[snip]
USER / PROJET... yes
[/snip]
Redis version >= 2.0.0? ... yes
Ruby version >= 2.0.0 ? ... yes (2.1.2)
Your git bin path is "/usr/bin/git"
Git version >= 1.7.10 ? ... yes (1.7.10)

Checking GitLab ... Finished
git@tst-gitlab:~/gitlab$ cat VERSION 
7.5.3