{"action":"created","issue":{"url":"https://api.github.com/repos/vmware/harbor/issues/4204","repository_url":"https://api.github.com/repos/vmware/harbor","labels_url":"https://api.github.com/repos/vmware/harbor/issues/4204/labels{/name}","comments_url":"https://api.github.com/repos/vmware/harbor/issues/4204/comments","events_url":"https://api.github.com/repos/vmware/harbor/issues/4204/events","html_url":"https://github.com/vmware/harbor/issues/4204","id":293308507,"number":4204,"title":"Installation problem with 1.3.0 and 1.4.0-rc1","user":{"login":"bergtwvd","id":10650187,"avatar_url":"https://avatars2.githubusercontent.com/u/10650187?v=4","gravatar_id":"","url":"https://api.github.com/users/bergtwvd","html_url":"https://github.com/bergtwvd","followers_url":"https://api.github.com/users/bergtwvd/followers","following_url":"https://api.github.com/users/bergtwvd/following{/other_user}","gists_url":"https://api.github.com/users/bergtwvd/gists{/gist_id}","starred_url":"https://api.github.com/users/bergtwvd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bergtwvd/subscriptions","organizations_url":"https://api.github.com/users/bergtwvd/orgs","repos_url":"https://api.github.com/users/bergtwvd/repos","events_url":"https://api.github.com/users/bergtwvd/events{/privacy}","received_events_url":"https://api.github.com/users/bergtwvd/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-01-31T20:56:35Z","updated_at":"2018-02-01T02:55:04Z","closed_at":null,"author_association":"NONE","body":"I follow the install/config instructions from the book. When I start it all up with install.sh I notice a problem in the database. Same problem for 1.3.0 and 1.4.0-rc1. Details below.\r\n\r\nWhen I place the volumes of the db and registry in a 75 Gb filesystem, problem persists.\r\n\r\n``\r\nInnoDB: Could not set the file size of './ibdata1'. Probably out of disk space\r\n``\r\n\r\nThere is enough disk space. On what filesystem does ibdata reside?\r\n\r\nAny idea of the cause and solution?\r\n\r\n\r\n1)Version of docker engine and docker-compose.\r\n````\r\nDocker version 1.11.2, build b9f10c9\r\ndocker-compose version 1.7.1, build 0a9ab35\r\n````\r\n2)Config files of harbor, you can get them by packaging \"harbor.cfg\" and files in the same directory, including subdirectory.\r\n````\r\n## Configuration file of Harbor\r\n\r\n#The IP address or hostname to access admin UI and registry service.\r\n#DO NOT use localhost or 127.0.0.1, because Harbor needs to be accessed by external clients.\r\nhostname = <snip/>\r\n\r\n#The protocol for accessing the UI and token/notification service, by default it is http.\r\n#It can be set to https if ssl is enabled on nginx.\r\nui_url_protocol = https\r\n\r\n#The password for the root user of mysql db, change this before any production use.\r\ndb_password = root123\r\n\r\n#Maximum number of job workers in job service\r\nmax_job_workers = 3\r\n\r\n#Determine whether or not to generate certificate for the registry's token.\r\n#If the value is on, the prepare script creates new root cert and private key\r\n#for generating token to access the registry. If the value is off the default key/cert will be used.\r\n#This flag also controls the creation of the notary signer's cert.\r\ncustomize_crt = off\r\n\r\n#The path of cert and key files for nginx, they are applied only the protocol is set to https\r\nssl_cert = /home/xxx/certs/domain.crt\r\nssl_cert_key = /home/xxx/certs/domain.key\r\n\r\n#The path of secretkey storage\r\nsecretkey_path = /data\r\n\r\n#Admiral's url, comment this attribute, or set its value to NA when Harbor is standalone\r\nadmiral_url = NA\r\n\r\n#The password of the Clair's postgres database, only effective when Harbor is deployed with Clair.\r\n#Please update it before deployment, subsequent update will cause Clair's API server and Harbor unable to access Clair's database.\r\nclair_db_password = password\r\n\r\n#Log files are rotated log_rotate_count times before being removed. If count is 0, old versions are removed rather than rotated.\r\nlog_rotate_count = 50\r\n#Log files are rotated only if they grow bigger than log_rotate_size bytes. If size is followed by k, the size is assumed to be in kilobytes.\r\n#If the M is used, the size is in megabytes, and if G is used, the size is in gigabytes. So size 100, size 100k, size 100M and size 100G\r\n#are all valid.\r\nlog_rotate_size = 200M\r\n\r\n#NOTES: The properties between BEGIN INITIAL PROPERTIES and END INITIAL PROPERTIES\r\n#only take effect in the first boot, the subsequent changes of these properties\r\n#should be performed on web ui\r\n\r\n#************************BEGIN INITIAL PROPERTIES************************\r\n\r\n#Email account settings for sending out password resetting emails.\r\n\r\n#Email server uses the given username and password to authenticate on TLS connections to host and act as identity.\r\n#Identity left blank to act as username.\r\nemail_identity =\r\n\r\nemail_server = mailhost2a.tno.nl\r\nemail_server_port = 25\r\nemail_username =\r\nemail_password =\r\nemail_from = Harbor admin <snip/>\r\nemail_ssl = false\r\nemail_insecure = false\r\n\r\n##The initial password of Harbor admin, only works for the first time when Harbor starts.\r\n#It has no effect after the first launch of Harbor.\r\n#Change the admin password from UI after launching Harbor.\r\nharbor_admin_password = Harbor12345\r\n\r\n##By default the auth mode is db_auth, i.e. the credentials are stored in a local database.\r\n#Set it to ldap_auth if you want to verify a user's credentials against an LDAP server.\r\nauth_mode = db_auth\r\n\r\n#The url for an ldap endpoint.\r\nldap_url = ldaps://ldap.mydomain.com\r\n\r\n#A user's DN who has the permission to search the LDAP/AD server.\r\n#If your LDAP/AD server does not support anonymous search, you should configure this DN and ldap_search_pwd.\r\n#ldap_searchdn = uid=searchuser,ou=people,dc=mydomain,dc=com\r\n\r\n#the password of the ldap_searchdn\r\n#ldap_search_pwd = password\r\n\r\n#The base DN from which to look up a user in LDAP/AD\r\nldap_basedn = ou=people,dc=mydomain,dc=com\r\n\r\n#Search filter for LDAP/AD, make sure the syntax of the filter is correct.\r\n#ldap_filter = (objectClass=person)\r\n\r\n# The attribute used in a search to match a user, it could be uid, cn, email, sAMAccountName or other attributes depending on your LDAP/AD\r\nldap_uid = uid\r\n\r\n#the scope to search for users, 0-LDAP_SCOPE_BASE, 1-LDAP_SCOPE_ONELEVEL, 2-LDAP_SCOPE_SUBTREE\r\nldap_scope = 2\r\n\r\n#Timeout (in seconds)  when connecting to an LDAP Server. The default value (and most reasonable) is 5 seconds.\r\nldap_timeout = 5\r\n\r\n#Verify certificate from LDAP server\r\nldap_verify_cert = true\r\n\r\n#Turn on or off the self-registration feature\r\nself_registration = on\r\n\r\n#The expiration time (in minute) of token created by token service, default is 30 minutes\r\ntoken_expiration = 30\r\n\r\n#The flag to control what users have permission to create projects\r\n#The default value \"everyone\" allows everyone to creates a project.\r\n#Set to \"adminonly\" so that only admin user can create project.\r\nproject_creation_restriction = adminonly\r\n\r\n#The follow configurations are for Harbor HA mode only\r\n#####################################################\r\n#the address of the mysql database.\r\ndb_host = mysql\r\n\r\n#The port of mysql database host\r\ndb_port = 3306\r\n\r\n#The user name of mysql database\r\ndb_user = root\r\n#The redis server address\r\nredis_url =\r\n\r\n#Clair DB host address\r\nclair_db_host = postgres\r\n\r\n#Clair DB connect port\r\nclair_db_port = 5432\r\n\r\n#Clair DB username\r\nclair_db_username = postgres\r\n\r\n#Clair default database\r\nclair_db = postgres\r\n################### end of HA section #####################\r\n\r\n#************************END INITIAL PROPERTIES************************\r\n\r\n#The following attributes only need to be set when auth mode is uaa_auth\r\nuaa_endpoint = uaa.mydomain.org\r\nuaa_clientid = id\r\nuaa_clientsecret = secret\r\nuaa_verify_cert = true\r\nuaa_ca_cert = /path/to/ca.pem\r\n\r\n\r\n### Docker Registry setting ###\r\n#registry_storage_provider can be: filesystem, s3, gcs, azure, etc.\r\nregistry_storage_provider_name = filesystem\r\n#registry_storage_provider_config is a comma separated \"key: value\" pairs, e.g. \"key1: value, key2: value2\".\r\n#Refer to https://docs.docker.com/registry/configuration/#storage for all available configuration.\r\nregistry_storage_provider_config =\r\n````\r\n\r\n\r\n3)Log files, you can get them by package the /var/log/harbor/ .\r\n````\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: Initializing database\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: 2018-01-31 20:45:18 139808786278336 [ERROR] InnoDB: preallocating 12582912 bytes for file ./ibdata1 failed with error 22\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: 2018-01-31 20:45:18 139808786278336 [ERROR] InnoDB: Could not set the file size of './ibdata1'. Probably out of disk space\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: 2018-01-31 20:45:18 139808786278336 [ERROR] InnoDB: Database creation was aborted with error Generic error. You may need to delete the ibdata\r\n1 file before trying to start up again.\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: 2018-01-31 20:45:18 139808786278336 [ERROR] Plugin 'InnoDB' init function returned error.\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: 2018-01-31 20:45:18 139808786278336 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: 2018-01-31 20:45:18 139808786278336 [ERROR] Unknown/unsupported storage engine: InnoDB\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: 2018-01-31 20:45:18 139808786278336 [ERROR] Aborting\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: Installation of system tables failed!  Examine the logs in\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: /var/lib/mysql/ for more information.\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: The problem could be conflicting information in an external\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: my.cnf files. You can ignore these by doing:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:     shell> /usr/bin/mysql_install_db --defaults-file=~/.my.cnf\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: You can also try to start the mysqld daemon with:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:     shell> /usr/sbin/mysqld --skip-grant --general-log &\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: and use the command line tool /usr/bin/mysql\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: to connect to the mysql database and look at the grant tables:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:     shell> /usr/bin/mysql -u root mysql\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:     mysql> show tables;\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: Try 'mysqld --help' if you have problems with paths.  Using\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: --general-log gives you a log in /var/lib/mysql/ that may be helpful.\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: The latest information about mysql_install_db is available at\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: https://mariadb.com/kb/en/installing-system-tables-mysql_install_db\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: MariaDB is hosted on launchpad; You can find the latest source and\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: email lists at http://launchpad.net/maria\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: Please check all of the above before submitting a bug report\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]: at http://mariadb.org/jira\r\nJan 31 21:45:18 172.20.0.1 docker/mysql[23304]:\r\nJan 31 21:45:19 172.20.0.1 docker/mysql[23304]: /usr/local/bin/docker-entrypoint.sh: running /docker-entrypoint-updatedb.d/upgrade.sh\r\nJan 31 21:45:19 172.20.0.1 docker/mysql[23304]: Maria DB flag not found, the DB was created in mysql image, running upgrade...\r\nJan 31 21:45:19 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:20 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:21 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:22 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:23 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:24 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:25 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:26 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:27 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:28 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:29 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:30 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:31 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:32 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:33 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:34 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:35 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:36 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:37 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:38 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:39 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:40 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:41 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:42 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:43 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:44 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:46 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:47 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:48 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:49 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:50 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:51 172.20.0.1 docker/mysql[23304]: MySQL failed to start.\r\nJan 31 21:45:51 172.20.0.1 docker/mysql[23304]: /usr/local/bin/docker-entrypoint.sh: running /docker-entrypoint-updatedb.d/upgrade.sh\r\nJan 31 21:45:51 172.20.0.1 docker/mysql[23304]: Maria DB flag not found, the DB was created in mysql image, running upgrade...\r\nJan 31 21:45:51 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:53 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:54 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:55 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:56 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:57 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:58 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:45:59 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:00 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:01 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:02 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:03 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:04 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:05 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:06 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:07 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:08 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:09 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:10 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:11 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:12 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:13 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:14 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:15 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:16 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:17 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:18 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:19 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\nJan 31 21:46:20 172.20.0.1 docker/mysql[23304]: Waiting for MySQL start...\r\n````\r\n"},"comment":{"url":"https://api.github.com/repos/vmware/harbor/issues/comments/362142684","html_url":"https://github.com/vmware/harbor/issues/4204#issuecomment-362142684","issue_url":"https://api.github.com/repos/vmware/harbor/issues/4204","id":362142684,"user":{"login":"ywk253100","id":5835782,"avatar_url":"https://avatars3.githubusercontent.com/u/5835782?v=4","gravatar_id":"","url":"https://api.github.com/users/ywk253100","html_url":"https://github.com/ywk253100","followers_url":"https://api.github.com/users/ywk253100/followers","following_url":"https://api.github.com/users/ywk253100/following{/other_user}","gists_url":"https://api.github.com/users/ywk253100/gists{/gist_id}","starred_url":"https://api.github.com/users/ywk253100/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ywk253100/subscriptions","organizations_url":"https://api.github.com/users/ywk253100/orgs","repos_url":"https://api.github.com/users/ywk253100/repos","events_url":"https://api.github.com/users/ywk253100/events{/privacy}","received_events_url":"https://api.github.com/users/ywk253100/received_events","type":"User","site_admin":false},"created_at":"2018-02-01T02:55:04Z","updated_at":"2018-02-01T02:55:04Z","author_association":"CONTRIBUTOR","body":"Did you upgrade to 1.3.0 and 1.4.0-rc1 from an old version or did a new installation without any existing data?"}}
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