Please also have a look at https://gitlab.com/gitlab-org/gitlab/-/issues/242388 Related to : https://gitlab.com/gitlab-org/charts/gitlab/-/issues/2113 ### Summary When you run apt-get update / upgrade on a production system today, you get into this problem ### Steps to reproduce I am not sure I can reproduce this bug without installing a new version. ### What is the current *bug* behavior? apt-get update && apt upgrade && gitlab-reconfigure pushed out this output: ``` Recipe: gitlab::database_migrations * bash[migrate gitlab-rails database] action run [execute] == 20200504191813 AddFingerprintToEvents: migrating =========================== -- column_exists?(:events, :fingerprint) -> 0.0030s -- add_column(:events, :fingerprint, :binary) -> 0.0095s -- transaction_open?() -> 0.0000s -- execute("ALTER TABLE events\nADD CONSTRAINT check_97e06e05ad\nCHECK ( octet_length(fingerprint) <= 128 )\nNOT VALID;\n") -> 0.0100s -- execute("ALTER TABLE events VALIDATE CONSTRAINT check_97e06e05ad;") -> 0.0162s == 20200504191813 AddFingerprintToEvents: migrated (0.0617s) ================== == 20200504200709 AddIndexOnFingerprintAndTargetTypeToEvents: migrating ======= -- transaction_open?() -> 0.0000s -- index_exists?(:events, [:target_type, :target_id, :fingerprint], {:using=>:btree, :unique=>true, :algorithm=>:concurrently}) -> 0.0113s -- add_index(:events, [:target_type, :target_id, :fingerprint], {:using=>:btree, :unique=>true, :algorithm=>:concurrently}) -> 0.0216s == 20200504200709 AddIndexOnFingerprintAndTargetTypeToEvents: migrated (0.0335s) == 20200515152649 EnableBtreeGistExtension: migrating ========================= -- execute("CREATE EXTENSION IF NOT EXISTS btree_gist") rake aborted! StandardError: An error has occurred, this and all later migrations canceled: PG::InsufficientPrivilege: ERROR: permission denied to create extension "btree_gist" HINT: Must be superuser to create this extension. /opt/gitlab/embedded/service/gitlab-rails/db/migrate/20200515152649_enable_btree_gist_extension.rb:7:in `up' /opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:54:in `block (3 levels) in <top (required)>' /opt/gitlab/embedded/bin/bundle:23:in `load' /opt/gitlab/embedded/bin/bundle:23:in `<main>' Caused by: ActiveRecord::StatementInvalid: PG::InsufficientPrivilege: ERROR: permission denied to create extension "btree_gist" HINT: Must be superuser to create this extension. /opt/gitlab/embedded/service/gitlab-rails/db/migrate/20200515152649_enable_btree_gist_extension.rb:7:in `up' /opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:54:in `block (3 levels) in <top (required)>' /opt/gitlab/embedded/bin/bundle:23:in `load' /opt/gitlab/embedded/bin/bundle:23:in `<main>' Caused by: PG::InsufficientPrivilege: ERROR: permission denied to create extension "btree_gist" HINT: Must be superuser to create this extension. /opt/gitlab/embedded/service/gitlab-rails/db/migrate/20200515152649_enable_btree_gist_extension.rb:7:in `up' /opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:54:in `block (3 levels) in <top (required)>' /opt/gitlab/embedded/bin/bundle:23:in `load' /opt/gitlab/embedded/bin/bundle:23:in `<main>' Tasks: TOP => db:migrate (See full trace by running task with --trace) ================================================================================ Error executing action `run` on resource 'bash[migrate gitlab-rails database]' ================================================================================ Mixlib::ShellOut::ShellCommandFailed ------------------------------------ Expected process to exit with [0], but received '1' ---- Begin output of "bash" "/tmp/chef-script20200829-1833-1bujtkw" ---- STDOUT: == 20200504191813 AddFingerprintToEvents: migrating =========================== -- column_exists?(:events, :fingerprint) -> 0.0030s -- add_column(:events, :fingerprint, :binary) -> 0.0095s -- transaction_open?() -> 0.0000s -- execute("ALTER TABLE events\nADD CONSTRAINT check_97e06e05ad\nCHECK ( octet_length(fingerprint) <= 128 )\nNOT VALID;\n") -> 0.0100s -- execute("ALTER TABLE events VALIDATE CONSTRAINT check_97e06e05ad;") -> 0.0162s == 20200504191813 AddFingerprintToEvents: migrated (0.0617s) ================== == 20200504200709 AddIndexOnFingerprintAndTargetTypeToEvents: migrating ======= -- transaction_open?() -> 0.0000s -- index_exists?(:events, [:target_type, :target_id, :fingerprint], {:using=>:btree, :unique=>true, :algorithm=>:concurrently}) -> 0.0113s -- add_index(:events, [:target_type, :target_id, :fingerprint], {:using=>:btree, :unique=>true, :algorithm=>:concurrently}) -> 0.0216s == 20200504200709 AddIndexOnFingerprintAndTargetTypeToEvents: migrated (0.0335s) == 20200515152649 EnableBtreeGistExtension: migrating ========================= -- execute("CREATE EXTENSION IF NOT EXISTS btree_gist") rake aborted! StandardError: An error has occurred, this and all later migrations canceled: PG::InsufficientPrivilege: ERROR: permission denied to create extension "btree_gist" HINT: Must be superuser to create this extension. /opt/gitlab/embedded/service/gitlab-rails/db/migrate/20200515152649_enable_btree_gist_extension.rb:7:in `up' /opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:54:in `block (3 levels) in <top (required)>' /opt/gitlab/embedded/bin/bundle:23:in `load' /opt/gitlab/embedded/bin/bundle:23:in `<main>' Caused by: ActiveRecord::StatementInvalid: PG::InsufficientPrivilege: ERROR: permission denied to create extension "btree_gist" HINT: Must be superuser to create this extension. /opt/gitlab/embedded/service/gitlab-rails/db/migrate/20200515152649_enable_btree_gist_extension.rb:7:in `up' /opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:54:in `block (3 levels) in <top (required)>' /opt/gitlab/embedded/bin/bundle:23:in `load' /opt/gitlab/embedded/bin/bundle:23:in `<main>' Caused by: PG::InsufficientPrivilege: ERROR: permission denied to create extension "btree_gist" HINT: Must be superuser to create this extension. /opt/gitlab/embedded/service/gitlab-rails/db/migrate/20200515152649_enable_btree_gist_extension.rb:7:in `up' /opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:54:in `block (3 levels) in <top (required)>' /opt/gitlab/embedded/bin/bundle:23:in `load' /opt/gitlab/embedded/bin/bundle:23:in `<main>' Tasks: TOP => db:migrate (See full trace by running task with --trace) STDERR: ---- End output of "bash" "/tmp/chef-script20200829-1833-1bujtkw" ---- Ran "bash" "/tmp/chef-script20200829-1833-1bujtkw" returned 1 Resource Declaration: --------------------- # In /opt/gitlab/embedded/cookbooks/cache/cookbooks/gitlab/recipes/database_migrations.rb 55: bash "migrate gitlab-rails database" do 56: code <<-EOH 57: set -e 58: log_file="#{node['gitlab']['gitlab-rails']['log_directory']}/gitlab-rails-db-migrate-$(date +%Y-%m-%d-%H-%M-%S).log" 59: umask 077 60: /opt/gitlab/bin/gitlab-rake gitlab:db:configure 2>& 1 | tee ${log_file} 61: STATUS=${PIPESTATUS[0]} 62: chown #{account_helper.gitlab_user}:#{account_helper.gitlab_group} ${log_file} 63: echo $STATUS > #{db_migrate_status_file} 64: exit $STATUS 65: EOH 66: environment env_variables unless env_variables.empty? 67: notifies :run, "execute[clear the gitlab-rails cache]", :immediately 68: dependent_services.each do |svc| 69: notifies :restart, svc, :immediately 70: end 71: not_if "(test -f #{db_migrate_status_file}) && (cat #{db_migrate_status_file} | grep -Fx 0)" 72: only_if { node['gitlab']['gitlab-rails']['auto_migrate'] } 73: end Compiled Resource: ------------------ # Declared in /opt/gitlab/embedded/cookbooks/cache/cookbooks/gitlab/recipes/database_migrations.rb:55:in `from_file' bash("migrate gitlab-rails database") do action [:run] default_guard_interpreter :default command nil backup 5 interpreter "bash" declared_type :bash cookbook_name "gitlab" recipe_name "database_migrations" code " set -e\n log_file=\"/var/log/gitlab/gitlab-rails/gitlab-rails-db-migrate-$(date +%Y-%m-%d-%H-%M-%S).log\"\n umask 077\n /opt/gitlab/bin/gitlab-rake gitlab:db:configure 2>& 1 | tee ${log_file}\n STATUS=${PIPESTATUS[0]}\n chown git:git ${log_file}\n echo $STATUS > /var/opt/gitlab/gitlab-rails/upgrade-status/db-migrate-47e6e804d9202096c772d1e85ab70abb-f4a969f7f49\n exit $STATUS\n" domain nil user nil not_if "(test -f /var/opt/gitlab/gitlab-rails/upgrade-status/db-migrate-47e6e804d9202096c772d1e85ab70abb-f4a969f7f49) && (cat /var/opt/gitlab/gitlab-rails/upgrade-status/db-migrate-47e6e804d9202096c772d1e85ab70abb-f4a969f7f49 | grep -Fx 0)" only_if { #code block } end System Info: ------------ chef_version=15.12.22 platform=ubuntu platform_version=18.04 ruby=ruby 2.6.6p146 (2020-03-31 revision 67876) [x86_64-linux] program_name=/opt/gitlab/embedded/bin/chef-client executable=/opt/gitlab/embedded/bin/chef-client Recipe: gitlab::puma * runit_service[puma] action restart (up to date) * runit_service[puma] action restart (up to date) Recipe: gitlab::sidekiq-cluster * sidekiq_service[sidekiq] action restart Recipe: <Dynamically Defined Resource> * service[sidekiq] action nothing (skipped due to action :nothing) * runit_service[sidekiq] action restart (up to date) (up to date) Recipe: gitlab::gitlab-rails * execute[clear the gitlab-rails cache] action run - execute /opt/gitlab/bin/gitlab-rake cache:clear Recipe: gitaly::enable * runit_service[gitaly] action hup - send hup to runit_service[gitaly] Running handlers: There was an error running gitlab-ctl reconfigure: bash[migrate gitlab-rails database] (gitlab::database_migrations line 55) had an error: Mixlib::ShellOut::ShellCommandFailed: Expected process to exit with [0], but received '1' ---- Begin output of "bash" "/tmp/chef-script20200829-1833-1bujtkw" ---- STDOUT: == 20200504191813 AddFingerprintToEvents: migrating =========================== -- column_exists?(:events, :fingerprint) -> 0.0030s -- add_column(:events, :fingerprint, :binary) -> 0.0095s -- transaction_open?() -> 0.0000s -- execute("ALTER TABLE events\nADD CONSTRAINT check_97e06e05ad\nCHECK ( octet_length(fingerprint) <= 128 )\nNOT VALID;\n") -> 0.0100s -- execute("ALTER TABLE events VALIDATE CONSTRAINT check_97e06e05ad;") -> 0.0162s == 20200504191813 AddFingerprintToEvents: migrated (0.0617s) ================== == 20200504200709 AddIndexOnFingerprintAndTargetTypeToEvents: migrating ======= -- transaction_open?() -> 0.0000s -- index_exists?(:events, [:target_type, :target_id, :fingerprint], {:using=>:btree, :unique=>true, :algorithm=>:concurrently}) -> 0.0113s -- add_index(:events, [:target_type, :target_id, :fingerprint], {:using=>:btree, :unique=>true, :algorithm=>:concurrently}) -> 0.0216s == 20200504200709 AddIndexOnFingerprintAndTargetTypeToEvents: migrated (0.0335s) == 20200515152649 EnableBtreeGistExtension: migrating ========================= -- execute("CREATE EXTENSION IF NOT EXISTS btree_gist") rake aborted! StandardError: An error has occurred, this and all later migrations canceled: PG::InsufficientPrivilege: ERROR: permission denied to create extension "btree_gist" HINT: Must be superuser to create this extension. /opt/gitlab/embedded/service/gitlab-rails/db/migrate/20200515152649_enable_btree_gist_extension.rb:7:in `up' /opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:54:in `block (3 levels) in <top (required)>' /opt/gitlab/embedded/bin/bundle:23:in `load' /opt/gitlab/embedded/bin/bundle:23:in `<main>' Caused by: ActiveRecord::StatementInvalid: PG::InsufficientPrivilege: ERROR: permission denied to create extension "btree_gist" HINT: Must be superuser to create this extension. /opt/gitlab/embedded/service/gitlab-rails/db/migrate/20200515152649_enable_btree_gist_extension.rb:7:in `up' /opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:54:in `block (3 levels) in <top (required)>' /opt/gitlab/embedded/bin/bundle:23:in `load' /opt/gitlab/embedded/bin/bundle:23:in `<main>' Caused by: PG::InsufficientPrivilege: ERROR: permission denied to create extension "btree_gist" HINT: Must be superuser to create this extension. /opt/gitlab/embedded/service/gitlab-rails/db/migrate/20200515152649_enable_btree_gist_extension.rb:7:in `up' /opt/gitlab/embedded/service/gitlab-rails/lib/tasks/gitlab/db.rake:54:in `block (3 levels) in <top (required)>' /opt/gitlab/embedded/bin/bundle:23:in `load' /opt/gitlab/embedded/bin/bundle:23:in `<main>' Tasks: TOP => db:migrate (See full trace by running task with --trace) STDERR: ---- End output of "bash" "/tmp/chef-script20200829-1833-1bujtkw" ---- Ran "bash" "/tmp/chef-script20200829-1833-1bujtkw" returned 1 Running handlers complete Chef Infra Client failed. 13 resources updated in 01 minutes 06 seconds ``` <details> <summary>Expand for output related to GitLab environment info</summary> <pre> System information System: Ubuntu 18.04 Current User: git Using RVM: no Ruby Version: 2.6.6p146 Gem Version: 2.7.10 Bundler Version:1.17.3 Rake Version: 12.3.3 Redis Version: 5.0.9 Git Version: 2.28.0 Sidekiq Version:5.2.9 Go Version: unknown GitLab information Version: 13.3.2 Revision: f4a969f7f49 Directory: /opt/gitlab/embedded/service/gitlab-rails DB Adapter: PostgreSQL DB Version: 12.4 URL: https://git.mydomain.com HTTP Clone URL: https://git.mydomain.com/some-group/some-project.git SSH Clone URL: git@git.mydomain.com:some-group/some-project.git Using LDAP: no Using Omniauth: yes Omniauth Providers: GitLab Shell Version: 13.6.0 Repository storage paths: - default: /home/git/repositories GitLab Shell path: /opt/gitlab/embedded/service/gitlab-shell Git: /opt/gitlab/embedded/bin/git </pre> </details> #### Results of GitLab application Check <!-- Input any relevant GitLab application check information if needed. --> <details> <summary>Expand for output related to the GitLab application check</summary> <pre> Checking GitLab subtasks ... Checking GitLab Shell ... GitLab Shell: ... GitLab Shell version >= 13.6.0 ? ... OK (13.6.0) Running /opt/gitlab/embedded/service/gitlab-shell/bin/check Internal API available: OK Redis available via internal API: OK gitlab-shell self-check successful Checking GitLab Shell ... Finished Checking Gitaly ... Gitaly: ... default ... OK Checking Gitaly ... Finished Checking Sidekiq ... Sidekiq: ... Running? ... yes Number of Sidekiq processes ... 1 Checking Sidekiq ... Finished Checking Incoming Email ... Incoming Email: ... Reply by email is disabled in config/gitlab.yml Checking Incoming Email ... Finished Checking LDAP ... LDAP: ... LDAP is disabled in config/gitlab.yml Checking LDAP ... Finished Checking GitLab App ... 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: ... 1/6 ... yes 7/7 ... yes 16/9 ... yes 16/10 ... yes 7/11 ... yes 16/19 ... yes 7/20 ... yes 7/21 ... yes 16/23 ... yes 16/24 ... yes 16/26 ... yes 16/27 ... yes 16/28 ... yes 16/29 ... yes 16/30 ... yes 16/31 ... yes 14/32 ... yes 16/33 ... yes 10/35 ... yes 16/36 ... yes 1/38 ... yes 1/40 ... yes 10/41 ... yes 14/42 ... yes 16/43 ... yes 16/44 ... yes 16/45 ... yes 14/46 ... yes 16/48 ... yes 16/49 ... yes 24/50 ... yes 16/51 ... yes 16/52 ... yes 1/53 ... yes 1/54 ... yes 1/55 ... yes 30/56 ... yes 30/58 ... yes 31/59 ... yes 31/61 ... yes 31/62 ... yes 32/63 ... yes 28/64 ... yes 32/65 ... yes 32/66 ... yes 30/67 ... yes 33/68 ... yes 26/69 ... yes 1/70 ... yes 32/71 ... yes 28/72 ... yes 32/73 ... yes 32/75 ... yes 32/76 ... yes 1/79 ... yes 38/80 ... yes 38/81 ... yes 1/82 ... yes 38/83 ... yes 38/84 ... yes 32/85 ... yes 32/86 ... yes 1/87 ... yes 1/88 ... yes 39/89 ... yes 32/90 ... yes 32/91 ... yes 32/94 ... yes 32/95 ... yes 1/96 ... yes 32/97 ... yes 1/98 ... yes 1/99 ... yes 43/100 ... yes 1/101 ... yes 43/102 ... yes 45/103 ... yes 38/104 ... yes 43/105 ... yes 45/107 ... yes 37/108 ... yes 32/109 ... yes 1/110 ... yes 32/111 ... yes 32/112 ... yes 1/113 ... yes Redis version >= 4.0.0? ... yes Ruby version >= 2.5.3 ? ... yes (2.6.6) Git version >= 2.24.0 ? ... yes (2.28.0) Git user has default SSH configuration? ... yes Active users: ... 11 Is authorized keys file accessible? ... yes GitLab configured to store new projects in hashed storage? ... yes All projects are in hashed storage? ... no Try fixing it: Please migrate all projects to hashed storage as legacy storage is deprecated in 13.0 and support will be removed in 14.0. For more information see: doc/administration/repository_storage_types.md Checking GitLab App ... Finished Checking GitLab subtasks ... Finished </pre> </details>