如何清理ibdata1

1， 加锁，然后全备份数据，可以用mysqldump，也可以使用其他的工具：

[root@localhost data]# mysqldump --all-databases > /root/all_databases.sql

2，修改my.cnf文件为你想要的大小

innodb_data_home_dir=/tmp/mysql-5.6/data
innodb_data_file_path=ibdata1:200M:autoextend:max:2G

注： ibdata1有最小限制

• For an innodb_page_size value of 16KB or less, the minimum file size is 3MB.
• For an innodb_page_size value of 32KB, the minimum file size is 6MB.
• For an innodb_page_size value of 64KB, the minimum file size is 12MB.

3， 删除ibdata1和ib_logfile0，ib_logfile1,ib_logfile2

[root@localhost data]# ls
a.sql     b.sql    ib_logfile0  itdb                        localhost-relay-bin.index  mysql-bin.000001  mysql-bin.000004  mysql-bin.000007  percona             test
auto.cnf  db2.sql  ib_logfile1  localhost.localdomain.pid   master.info                mysql-bin.000002  mysql-bin.000005  mysql-bin.000008  performance_schema
books     ibdata1  ib_logfile2  localhost-relay-bin.000008  mysql                      mysql-bin.000003  mysql-bin.000006  mysql-bin.index   relay-log.info

[root@localhost data]#
[root@localhost data]# rm -rf ibdata1
[root@localhost data]# rm -rf ib_log*

[root@localhost data]# ls
a.sql     books  db2.sql  localhost.localdomain.pid   localhost-relay-bin.index  mysql             mysql-bin.000002  mysql-bin.000004  mysql-bin.000006  mysql-bin.000008  percona             relay-log.info
auto.cnf  b.sql  itdb     localhost-relay-bin.000008  master.info                mysql-bin.000001  mysql-bin.000003  mysql-bin.000005  mysql-bin.000007  mysql-bin.index   performance_schema  test
[root@localhost data]#

4，重启mysql,此时发现ibdata1变成我们想要的大小了；

[root@localhost data]# service mysqld restart
Shutting down MySQL.... SUCCESS!
Starting MySQL... SUCCESS!
[root@localhost data]# du -sh ibdata1
201M	ibdata1
[root@localhost data]#

5， 登陆mysql,删除数据库，此时发现无法删除；因为数据字典所在的表空间被删了；

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| books              |
| itdb               |
| mysql              |
| percona            |
| performance_schema |
| test               |
+--------------------+
7 rows in set (0.00 sec)

mysql> drop database books;
ERROR 1010 (HY000): Error dropping database (can't rmdir './books', errno: 39)
mysql>

此时把database文件夹移走；performance_schema不要动，其他的都移走

root@localhost data]# ls
auto.cnf  ibdata1      ib_logfile1  itdb                       localhost-relay-bin.000004  master.info  mysql-bin.000001  mysql-bin.000003  mysql-bin.index  performance_schema  test
books     ib_logfile0  ib_logfile2  localhost.localdomain.pid  localhost-relay-bin.index   mysql        mysql-bin.000002  mysql-bin.000004  percona          relay-log.info
[root@localhost data]# mkdir /bak
[root@localhost data]# mv itdb books mysql percona test /bak
[root@localhost data]# ls
auto.cnf  ib_logfile0  ib_logfile2                localhost-relay-bin.000004  master.info       mysql-bin.000002  mysql-bin.000004  performance_schema
ibdata1   ib_logfile1  localhost.localdomain.pid  localhost-relay-bin.index   mysql-bin.000001  mysql-bin.000003  mysql-bin.index   relay-log.info
[root@localhost data]#

移完之后，查看系统只有information_schema和performance_schema2个库；
然后进行恢复数据

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| performance_schema |
+--------------------+
2 rows in set (0.00 sec)

mysql>
[1]+  Stopped                 mysql  (wd: /tmp/mysql-5.6/data)
(wd now: ~)
[root@localhost ~]#
[root@localhost ~]#
[root@localhost ~]# mysql -e "source /root/all_databases.sql"  > source.log

然后查看数据：

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| books              |
| itdb               |
| mysql              |
| percona            |
| performance_schema |
| test               |
+--------------------+
7 rows in set (0.00 sec)

mysql> use itdb
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Database changed
mysql> show tables;
+------------------+
| Tables_in_itdb   |
+------------------+
| contact          |
| customers        |
| kepler_promotion |
| orderitems       |
| orders           |
| productnotes     |
| products         |
| shopping         |
| tt               |
| vendors          |
+------------------+
mysql> select * from contact limit 5;
+----+---------+-------+------+---------------+
| id | user_id | name  | ext  | email         |
+----+---------+-------+------+---------------+
|  0 |       0 | NULL  | NULL | NULL          |
|  1 |       1 | user1 | 2000 | user1@163.com |
|  2 |       2 | user2 | 2001 | user2@163.com |
|  3 |       3 | user3 | 2002 | user1@164.com |
|  4 |       4 | user4 | 2003 | user2@164.com |
+----+---------+-------+------+---------------+
5 rows in set (0.01 sec)

OK，完成；
重启下服务，查看错误日志，看是否有ERR；经查没有，OK，完成

2018-01-21 13:06:42 127993 [Note] Plugin 'FEDERATED' is disabled.
2018-01-21 13:06:42 127993 [Note] InnoDB: Using atomics to ref count buffer pool pages
2018-01-21 13:06:42 127993 [Note] InnoDB: The InnoDB memory heap is disabled
2018-01-21 13:06:42 127993 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2018-01-21 13:06:42 127993 [Note] InnoDB: Memory barrier is not used
2018-01-21 13:06:42 127993 [Note] InnoDB: Compressed tables use zlib 1.2.3
2018-01-21 13:06:42 127993 [Note] InnoDB: Using Linux native AIO
2018-01-21 13:06:42 127993 [Note] InnoDB: Using CPU crc32 instructions
2018-01-21 13:06:42 127993 [Note] InnoDB: Initializing buffer pool, size = 64.0M
2018-01-21 13:06:42 127993 [Note] InnoDB: Completed initialization of buffer pool
2018-01-21 13:06:42 127993 [Note] InnoDB: Highest supported file format is Barracuda.
2018-01-21 13:06:42 127993 [Note] InnoDB: 128 rollback segment(s) are active.
2018-01-21 13:06:42 127993 [Note] InnoDB: Waiting for purge to start
2018-01-21 13:06:42 127993 [Note] InnoDB: 5.6.36 started; log sequence number 1854145
2018-01-21 13:06:42 127993 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
2018-01-21 13:06:42 127993 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
2018-01-21 13:06:42 127993 [Note] Server socket created on IP: '0.0.0.0'.
2018-01-21 13:06:42 127993 [Warning] Neither --relay-log nor --relay-log-index were used; so replication may break when this MySQL server acts as a slave and has his hostname changed!! Please use '--relay-log=localhost-relay-bin' to avoid this problem.
2018-01-21 13:06:42 127993 [Note] Event Scheduler: Loaded 0 events
2018-01-21 13:06:42 127993 [Note] /tmp/mysql-5.6/bin/mysqld: ready for connections.
Version: '5.6.36-log'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MySQL Community Server (GPL)
2018-01-21 13:06:42 127993 [Warning] Storing MySQL user name or password information in the master info repository is not secure and is therefore not recommended. Please consider using the USER and PASSWORD connection options for START SLAVE; see the 'START SLAVE Syntax' in the MySQL Manual for more information.
2018-01-21 13:06:42 127993 [Warning] Slave SQL: If a crash happens this configuration does not guarantee that the relay log info will be consistent, Error_code: 0
2018-01-21 13:06:42 127993 [Note] Slave SQL thread initialized, starting replication in log 'mysql-bin.000003' at position 1205, relay log './localhost-relay-bin.000001' position: 4

我这是mysql 5.6版本，经测试mysql 5.7版本也是一样的方法，移动的时候多了个sys的库也要一起移走；其他一样；