It seems that your new MySQL doesn't have some of the required mysql system database tables, most of them are handled by InnoDB, e.g.:
*May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.595846Z 0 [Warning] InnoDB: Cannot open table mysql/plugin from the internal data dictionary of InnoDB though the .frm file for the table exists. Please refer to http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for how to resolve the issue. May 15 09:41:27 anakin mysqld: mysqld: Table 'mysql.plugin' doesn't exist May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.595877Z 0 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.* *May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.596419Z 0 [Warning] InnoDB: Cannot open table mysql/gtid_executed from the internal data dictionary of InnoDB though the .frm file for the table exists. Please refer to http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for how to resolve the issue. May 15 09:41:27 anakin mysqld: mysqld: Table 'mysql.gtid_executed' doesn't exist May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.596439Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.* As you're trying MySQL 5.7.7, I recommend that you to have a read on this page below: https://dev.mysql.com/doc/refman/5.7/en/data-directory-initialization-mysqld.html -- *Wagner Bianchi, +55.31.8654.9510* Oracle ACE Director <https://apex.oracle.com/pls/otn/f?p=19297:4:105567988301604::NO:4:P4_ID:4541>, MySQL Certified Professional Percona MySQL Forum <http://www.percona.com/forums/> Community V.I.P. Email: m...@wagnerbianchi.com Skype: wbianchijr 2015-05-15 4:57 GMT-03:00 Jørn Dahl-Stamnes <sq...@dahl-stamnes.net>: > Hello, > > I have reinstalled a test server after a disk crash. I upgraded from an > older Fedora Core (don't > remember the version) to Fedora Core 21. > > Then I installed Mysql 5.7.7 from RPM. I'm able to start it but mysql does > not use my /etc/my.cnf > file and I do not find any other on my system. > > After doing a 'yum install ...' I started it without a my.cnf file. It > seem to start OK and all the > database files++ was added to /var/lib/mysql. > > Since I got a SSD disk where I want to locate the databases, I stopped > mysql and moved the file to > this disk and added links (just as I did on the old system). > I removed all ib* files and added my myc.fn file (it contain info about > ibdata files etc) and then > tried to start it - no luck. > > Base on the entries in /var/log/messages, it does not seem to use the > /etc/my.cnf file. There is > also a few warnings which I'm not sure how to fix. > > Any suggestions what's wrong? > > > My my.cnf file: > # The MySQL server > [mysqld] > port = 3306 > socket = /tmp/mysql.sock > > skip-external-locking > key_buffer_size = 384M > max_allowed_packet = 32M > table_open_cache = 512 > sort_buffer_size = 2M > read_buffer_size = 2M > read_rnd_buffer_size = 8M > myisam_sort_buffer_size = 64M > thread_cache_size = 8 > query_cache_size = 32M > # Try number of CPU's*2 for thread_concurrency > thread_concurrency = 16 > max_connections = 50 > > log-bin=/var/mysql/mysql-bin > > server-id = 1 > > binlog_format=mixed > > # Innodb settings. > > # Open files. > innodb_open_files = 2048 > open_files_limit = 8096 > > innodb_data_home_dir = /data/mysql/data > innodb_data_file_path = > ibdata1:20G;ibdata2:20G;ibdata3:20G;ibdata4:20G:autoextend > innodb_file_per_table = 0 > innodb_autoextend_increment = 256 > > innodb_log_group_home_dir = /data/mysql/data > > # You can set .._buffer_pool_size up to 50 - 80 % > # of RAM but beware of setting memory usage too high. > innodb_buffer_pool_size = 25G > > # Set .._log_file_size to 25 % of buffer pool size > innodb_log_file_size = 300M > innodb_log_files_in_group = 2 > innodb_log_buffer_size = 128M > > innodb_flush_log_at_trx_commit = 1 > innodb_support_xa = 0 > innodb_flush_method = O_DIRECT > innodb_lock_wait_timeout = 50 > innodb_fast_shutdown = 0 > > > > From /var/log/messages: > > > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.255284Z 0 [Warning] > TIMESTAMP with implicit > DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp > server option (see > documentation for more details). > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.256631Z 0 [Note] > /usr/sbin/mysqld (mysqld 5.7.7- > rc) starting as process 1528 ... > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.265686Z 0 [Note] > InnoDB: Mutexes and rw_locks use > GCC atomic builtins > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.266263Z 0 [Note] > InnoDB: Uses event mutexes > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.266661Z 0 [Note] > InnoDB: GCC builtin > __atomic_thread_fence() is used for memory barrier > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.267045Z 0 [Note] > InnoDB: Compressed tables use > zlib 1.2.3 > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.267432Z 0 [Note] > InnoDB: Using Linux native AIO > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.268269Z 0 [Note] > InnoDB: Number of pools: 1 > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.268804Z 0 [Note] > InnoDB: Using CPU crc32 > instructions > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.270686Z 0 [Note] > InnoDB: Initializing buffer > pool, total size = 128M, instances = 1, chunk size = 128M > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.298852Z 0 [Note] > InnoDB: Completed initialization > of buffer pool > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.353601Z 0 [Note] > InnoDB: If the mysqld execution > user is authorized, page cleaner thread priority can be changed. See the > man page of setpriority(). > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.356077Z 0 [Note] > InnoDB: Highest supported file > format is Barracuda. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.361383Z 0 [Note] > InnoDB: Log scan progressed past > the checkpoint lsn 1210467 > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.361927Z 0 [Note] > InnoDB: Doing recovery: scanned > up to log sequence number 1210476 > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.362672Z 0 [Note] > InnoDB: Doing recovery: scanned > up to log sequence number 1210476 > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.363083Z 0 [Note] > InnoDB: Database was not > shutdown normally! > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.363456Z 0 [Note] > InnoDB: Starting crash recovery. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.484951Z 0 [Note] > InnoDB: Removed temporary > tablespace data file: "ibtmp1" > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.488568Z 0 [Note] > InnoDB: Creating shared > tablespace for temporary tables > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.489014Z 0 [Note] > InnoDB: Setting file './ibtmp1' > size to 12 MB. Physically writing the file full; Please wait ... > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.536654Z 0 [Note] > InnoDB: File './ibtmp1' size is > now 12 MB. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.538070Z 0 [Note] > InnoDB: 96 redo rollback > segment(s) found. 96 redo rollback segment(s) are active. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.538087Z 0 [Note] > InnoDB: 32 non-redo rollback > segment(s) are active. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.538301Z 0 [Note] > InnoDB: Waiting for purge to > start > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.594640Z 0 [Note] > InnoDB: 5.7.7 started; log > sequence number 1210476 > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.595238Z 0 [Note] > InnoDB: Loading buffer pool(s) > from .//ib_buffer_pool > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.595286Z 0 [ERROR] > InnoDB: Cannot open > './/ib_buffer_pool' for reading: No such file or directory > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.595415Z 0 [Note] Plugin > 'FEDERATED' is disabled. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.595846Z 0 [Warning] > InnoDB: Cannot open table > mysql/plugin from the internal data dictionary of InnoDB though the .frm > file for the table exists. > Please refer to > http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for > how to > resolve the issue. > May 15 09:41:27 anakin mysqld: mysqld: Table 'mysql.plugin' doesn't exist > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.595877Z 0 [ERROR] Can't > open the mysql.plugin > table. Please run mysql_upgrade to create it. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.596419Z 0 [Warning] > InnoDB: Cannot open table > mysql/gtid_executed from the internal data dictionary of InnoDB though the > .frm file for the table > exists. Please refer to > http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for how > to resolve the issue. > May 15 09:41:27 anakin mysqld: mysqld: Table 'mysql.gtid_executed' doesn't > exist > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.596439Z 0 [Warning] > Gtid table is not ready to be > used. Table 'mysql.gtid_executed' cannot be opened. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.596483Z 0 [Warning] > Failed to setup SSL > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.596493Z 0 [Warning] SSL > error: SSL context is not > usable without certificate and private key > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.596915Z 0 [Note] Server > hostname (bind-address): > '*'; port: 3306 > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.596952Z 0 [Note] IPv6 > is available. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.596967Z 0 [Note] - > '::' resolves to '::'; > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.596976Z 0 [Note] Server > socket created on IP: > '::'. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.599237Z 0 [Warning] > InnoDB: Cannot open table > mysql/server_cost from the internal data dictionary of InnoDB though the > .frm file for the table > exists. Please refer to > http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for how > to resolve the issue. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.599259Z 0 [Warning] > Failed to open optimizer cost > constant tables > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.600318Z 0 [Warning] > InnoDB: Cannot open table > mysql/time_zone_leap_second from the internal data dictionary of InnoDB > though the .frm file for the > table exists. Please refer to > http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for > how to resolve the issue. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.600340Z 0 [Warning] > Can't open and lock time zone > table: Table 'mysql.time_zone_leap_second' doesn't exist trying to live > without them > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.604819Z 0 [Warning] > InnoDB: Cannot open table > mysql/servers from the internal data dictionary of InnoDB though the .frm > file for the table exists. > Please refer to > http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for > how to > resolve the issue. > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.604842Z 0 [ERROR] Can't > open and lock privilege > tables: Table 'mysql.servers' doesn't exist > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.616215Z 0 [Note] Event > Scheduler: Loaded 0 events > May 15 09:41:27 anakin mysqld: 2015-05-15T07:41:27.619566Z 0 [Note] > /usr/sbin/mysqld: ready for > connections. > May 15 09:41:27 anakin mysqld: Version: '5.7.7-rc' socket: > '/var/lib/mysql/mysql.sock' port: 3306 > MySQL Community Server (GPL) > > > [Comment: This part seem to repeat itself until I stop the mysql daemon] > > May 15 09:42:57 anakin systemd: mysqld.service start operation timed out. > Terminating. > May 15 09:42:57 anakin systemd: Failed to start MySQL Server. > May 15 09:42:57 anakin systemd: Unit mysqld.service entered failed state. > May 15 09:42:57 anakin systemd: mysqld.service failed. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.651714Z 0 [Warning] > TIMESTAMP with implicit > DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp > server option (see > documentation for more details). > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.652654Z 0 [Note] > /usr/sbin/mysqld (mysqld 5.7.7- > rc) starting as process 1576 ... > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.661812Z 0 [Note] > InnoDB: Mutexes and rw_locks use > GCC atomic builtins > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.661873Z 0 [Note] > InnoDB: Uses event mutexes > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.661883Z 0 [Note] > InnoDB: GCC builtin > __atomic_thread_fence() is used for memory barrier > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.661891Z 0 [Note] > InnoDB: Compressed tables use > zlib 1.2.3 > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.661898Z 0 [Note] > InnoDB: Using Linux native AIO > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.662681Z 0 [Note] > InnoDB: Number of pools: 1 > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.662944Z 0 [Note] > InnoDB: Using CPU crc32 > instructions > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.665426Z 0 [Note] > InnoDB: Initializing buffer > pool, total size = 128M, instances = 1, chunk size = 128M > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.697243Z 0 [Note] > InnoDB: Completed initialization > of buffer pool > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.717179Z 0 [Note] > InnoDB: Highest supported file > format is Barracuda. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.722580Z 0 [Note] > InnoDB: If the mysqld execution > user is authorized, page cleaner thread priority can be changed. See the > man page of setpriority(). > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.725961Z 0 [Note] > InnoDB: Log scan progressed past > the checkpoint lsn 1210893 > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.728948Z 0 [Note] > InnoDB: Doing recovery: scanned > up to log sequence number 1210902 > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.729312Z 0 [Note] > InnoDB: Doing recovery: scanned > up to log sequence number 1210902 > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.729323Z 0 [Note] > InnoDB: Database was not > shutdown normally! > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.729330Z 0 [Note] > InnoDB: Starting crash recovery. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.851622Z 0 [Note] > InnoDB: Removed temporary > tablespace data file: "ibtmp1" > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.852038Z 0 [Note] > InnoDB: Creating shared > tablespace for temporary tables > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.852357Z 0 [Note] > InnoDB: Setting file './ibtmp1' > size to 12 MB. Physically writing the file full; Please wait ... > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.906373Z 0 [Note] > InnoDB: File './ibtmp1' size is > now 12 MB. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.907726Z 0 [Note] > InnoDB: 96 redo rollback > segment(s) found. 96 redo rollback segment(s) are active. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.907736Z 0 [Note] > InnoDB: 32 non-redo rollback > segment(s) are active. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.907944Z 0 [Note] > InnoDB: Waiting for purge to > start > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.964668Z 0 [Note] > InnoDB: 5.7.7 started; log > sequence number 1210902 > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.968579Z 0 [Note] > InnoDB: Loading buffer pool(s) > from .//ib_buffer_pool > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.968625Z 0 [ERROR] > InnoDB: Cannot open > './/ib_buffer_pool' for reading: No such file or directory > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.970723Z 0 [Note] Plugin > 'FEDERATED' is disabled. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.971171Z 0 [Warning] > InnoDB: Cannot open table > mysql/plugin from the internal data dictionary of InnoDB though the .frm > file for the table exists. > Please refer to > http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for > how to > resolve the issue. > May 15 09:42:57 anakin mysqld: mysqld: Table 'mysql.plugin' doesn't exist > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.971202Z 0 [ERROR] Can't > open the mysql.plugin > table. Please run mysql_upgrade to create it. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.975105Z 0 [Warning] > InnoDB: Cannot open table > mysql/gtid_executed from the internal data dictionary of InnoDB though the > .frm file for the table > exists. Please refer to > http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for how > to resolve the issue. > May 15 09:42:57 anakin mysqld: mysqld: Table 'mysql.gtid_executed' doesn't > exist > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.975144Z 0 [Warning] > Gtid table is not ready to be > used. Table 'mysql.gtid_executed' cannot be opened. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.975196Z 0 [Warning] > Failed to setup SSL > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.975206Z 0 [Warning] SSL > error: SSL context is not > usable without certificate and private key > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.975663Z 0 [Note] Server > hostname (bind-address): > '*'; port: 3306 > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.975705Z 0 [Note] IPv6 > is available. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.975725Z 0 [Note] - > '::' resolves to '::'; > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.975733Z 0 [Note] Server > socket created on IP: > '::'. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.984931Z 0 [Warning] > InnoDB: Cannot open table > mysql/server_cost from the internal data dictionary of InnoDB though the > .frm file for the table > exists. Please refer to > http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for how > to resolve the issue. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.984972Z 0 [Warning] > Failed to open optimizer cost > constant tables > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.985645Z 0 [Warning] > InnoDB: Cannot open table > mysql/time_zone_leap_second from the internal data dictionary of InnoDB > though the .frm file for the > table exists. Please refer to > http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for > how to resolve the issue. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.985661Z 0 [Warning] > Can't open and lock time zone > table: Table 'mysql.time_zone_leap_second' doesn't exist trying to live > without them > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.986086Z 0 [Warning] > InnoDB: Cannot open table > mysql/servers from the internal data dictionary of InnoDB though the .frm > file for the table exists. > Please refer to > http://dev.mysql.com/doc/refman/5.7/en/innodb-troubleshooting.html for > how to > resolve the issue. > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.986100Z 0 [ERROR] Can't > open and lock privilege > tables: Table 'mysql.servers' doesn't exist > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.997527Z 0 [Note] Event > Scheduler: Loaded 0 events > May 15 09:42:57 anakin mysqld: 2015-05-15T07:42:57.997956Z 0 [Note] > /usr/sbin/mysqld: ready for > connections. > May 15 09:42:57 anakin mysqld: Version: '5.7.7-rc' socket: > '/var/lib/mysql/mysql.sock' port: 3306 > MySQL Community Server (GPL) > > > > -- > Jørn Dahl-Stamnes > homepage: http://photo.dahl-stamnes.net/ > > -- > MySQL General Mailing List > For list archives: http://lists.mysql.com/mysql > To unsubscribe: http://lists.mysql.com/mysql > >
