1

According to mysqltunner.pl I have 177 Fragmented tables. I have over 5000 tables and 200 databases.

If I run optimize table on each of them, do you think I should take down the application to prevent reads and writes while I do this? I know that optimize locks the table, but if it is a pretty quick operation I don't know if it was cause any problems.

2

You can optimize a table without interrupting service by using pt-online-schema-change:

$ pt-online-schema-change --alter="ENGINE=InnoDB" --execute D=sakila,t=actor

Also, MySQL 5.6.17 supports OPTIMIZE as an online DDL change, allowing concurrent DML.

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0

IMHO when you maintain your DB in this invasive way, you must stop the application.

Send a communication to your customers so they be able to plan their activities.

You can't stop your application when the maintenance task are very fastes.

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