你可以看下ibdata1文件里都是啥(innochecksum --page-type-summary ibdata),
可以把数据单独出去, 把undo也单独出去.

(venv) 14:57:13 [root@ddcw21 ei]#innochecksum --page-type-summary  /data/mysql_3308/mysqldata/ibdata1 

File::/data/mysql_3308/mysqldata/ibdata1
================PAGE TYPE SUMMARY==============
#PAGE_COUNT	PAGE_TYPE
===============================================
     444	Index page
   53212	Undo log page
     614	Inode page
     217	Insert buffer free list page
    3462	Freshly allocated page
       4	Insert buffer bitmap
     154	System page
       1	Transaction system page
       1	File Space Header
       3	Extent descriptor page
       0	BLOB page
       0	Compressed BLOB page
       0	Other type of page
===============================================
Additional information:
Undo page type: 734 insert, 52478 update, 0 other
Undo page state: 0 active, 411 cached, 0 to_free, 52327 to_purge, 0 prepared, 474 other

重新安装一下，每个表空间一个文件就可以了 

设置成独立表空间innodb_file_per_table=1迁移一下数据

重新安装一下，每个表空间一个文件就可以了