Fresh Install: ERROR! The server quit without updating PID file

[jbatson]

Starting MySQL (Percona Server)… ERROR! The server quit without updating PID file (/var/lib/mysql/mysql.pid).

Fresh install on new server. Created config file using the configuration wizard.

Server will not start. Tried permissions, removing ib_logfile’s.

Server is amazon small instance. Any help would be great.

Log file:

150821 16:26:30 mysqld_safe mysqld from pid file /var/lib/mysql/mysql.pid ended
150821 16:27:24 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql/
2015-08-21 16:27:25 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2015-08-21 16:27:25 0 [Warning] ‘ERROR_FOR_DIVISION_BY_ZERO’ is deprecated and will be removed in a future release.
2015-08-21 16:27:25 0 [Note] /usr/sbin/mysqld (mysqld 5.6.25-73.1-log) starting as process 5547 …
2015-08-21 16:27:25 5547 [Warning] Using unique option prefix myisam-recover instead of myisam-recover-options is deprecated and will be removed in a future release. Please use the full name instead.
2015-08-21 16:27:25 5547 [Note] Plugin ‘FEDERATED’ is disabled.
2015-08-21 16:27:25 5547 [Note] InnoDB: Using atomics to ref count buffer pool pages
2015-08-21 16:27:25 5547 [Note] InnoDB: The InnoDB memory heap is disabled
2015-08-21 16:27:25 5547 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2015-08-21 16:27:25 5547 [Note] InnoDB: Memory barrier is not used
2015-08-21 16:27:25 5547 [Note] InnoDB: Compressed tables use zlib 1.2.3
2015-08-21 16:27:25 5547 [Note] InnoDB: Using Linux native AIO
2015-08-21 16:27:25 5547 [Note] InnoDB: Using CPU crc32 instructions
2015-08-21 16:27:25 5547 [Note] InnoDB: Initializing buffer pool, size = 1.4G
2015-08-21 16:27:25 5547 [Note] InnoDB: Completed initialization of buffer pool
2015-08-21 16:27:25 5547 [Note] InnoDB: Restoring page 0 of tablespace 0
2015-08-21 16:27:25 5547 [Warning] InnoDB: Doublewrite does not have page_no=0 of space: 0
2015-08-21 16:27:25 5547 [ERROR] InnoDB: space header page consists of zero bytes in data file ./ibdata1
2015-08-21 16:27:25 5547 [ERROR] InnoDB: Could not open or create the system tablespace. If you tried to add new data files to the system tablespace, and it failed here, you should now edit innodb_data_file_path in my.cnf back to what it was,
and remove the new ibdata files InnoDB created in this failed attempt. InnoDB only wrote those files full of zeros, but did not yet use them in any way. But be careful: do not remove old data files which contain your precious data!
2015-08-21 16:27:25 5547 [ERROR] Plugin ‘InnoDB’ init function returned error.
2015-08-21 16:27:25 5547 [ERROR] Plugin ‘InnoDB’ registration as a STORAGE ENGINE failed.
2015-08-21 16:27:25 5547 [ERROR] Unknown/unsupported storage engine: InnoDB
2015-08-21 16:27:25 5547 [ERROR] Aborting

2015-08-21 16:27:25 5547 [Note] Binlog end
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘partition’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘ARCHIVE’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘BLACKHOLE’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘PERFORMANCE_SCHEMA’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_CHANGED_PAGES’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_SYS_DATAFILES’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_SYS_TABLESPACES’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_SYS_FOREIGN_COLS’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_SYS_FOREIGN’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_SYS_FIELDS’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_SYS_COLUMNS’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_SYS_INDEXES’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_SYS_TABLESTATS’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_SYS_TABLES’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_FT_INDEX_TABLE’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_FT_INDEX_CACHE’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_FT_CONFIG’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_FT_BEING_DELETED’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_FT_DELETED’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_FT_DEFAULT_STOPWORD’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_METRICS’
2015-08-21 16:27:25 5547 [Note] Shutting down plugin ‘INNODB_BUFFER_POOL_STATS’

[jbatson]

Found that is has something to do with my.cnf file. Not sure what it is though, have 5.6 running on another server with same cnf file with no issues. Renamed file and started fine.

Generated by Percona Configuration Wizard (http://tools.percona.com/) version REL5-20120208

Configuration name percona-server generated for at 2015-08-21 16:00:01

[mysql]

CLIENT

port = 3306
socket = /var/lib/mysql/mysql.sock

[mysqld]

GENERAL

user = mysql
default-storage-engine = InnoDB
socket = /var/lib/mysql/mysql.sock
pid-file = /var/lib/mysql/mysql.pid

MyISAM

key-buffer-size = 32M
myisam-recover = FORCE,BACKUP

SAFETY

max-allowed-packet = 16M
max-connect-errors = 1000000
sql-mode = STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_ AUTO_CREATE_USER,NO_AUTO_VALUE_ON_ZERO,NO_ENGINE_S UBSTITUTION,ONLY_FULL_GROUP_BY
sysdate-is-now = 1

DATA STORAGE

datadir = /var/lib/mysql/

BINARY LOGGING

log-bin = /var/lib/mysql/mysql-bin
expire-logs-days = 14
sync-binlog = 1

CACHES AND LIMITS

tmp-table-size = 32M
max-heap-table-size = 32M
query-cache-type = 0
query-cache-size = 0
max-connections = 500
thread-cache-size = 50
open-files-limit = 65535
table-definition-cache = 1024
table-open-cache = 2048

INNODB

innodb-flush-method = O_DIRECT
innodb-log-files-in-group = 2
innodb-log-file-size = 128M
innodb-flush-log-at-trx-commit = 1
innodb-file-per-table = 1
innodb-buffer-pool-size = 1456M

LOGGING

log-error = /var/lib/mysql/mysql-error.log
log-queries-not-using-indexes = 1
slow-query-log = 1
slow-query-log-file = /var/lib/mysql/mysql-slow.log

[jbatson]

Not sure what issue was. Uninstalled then re-installed, added my.cnf, started server working fine.