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Would performing daily optimizations of tables increase performance for MySQL and InnoDB? I have never did this before, but I have seen this module for Drupal http://drupal.org/project/db_maintenance, and it looks promising.

PS: As I learned, OPTIMIZE TABLE liberates overhead. However, I double checked the overhead column in mysql and it is all empty for my innodb tables ... So, I guess this may not be necessary.

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MyISAM

Doing OPTIMIZE TABLE mydb.mytable; performs two basic operations

ALTER TABLE mydb.mytable ENGINE=MyISAM;
ANALYZE TABLE mydb.mytable;

This definitely cleans up table fragmentation and computes fresh statistics for indexes

InnoDB

Doing OPTIMIZE TABLE mydb.mytable; performs two basic operations

ALTER TABLE mydb.mytable ENGINE=InnoDB;
ANALYZE TABLE mydb.mytable;

While this eliminates fragmentation, ANAYLZE TABLE is complete useless for InnoDB. I wrote about this a long time ago:

If your data growth rate is very small (or in other words, your dataset stays basically the same size for months at a time), then defragmenting tables would just be overkill. You should probably focus on tuning InnoDB's other aspects (See my Aug 04, 2011 post: Optimizing InnoDB default settings)

I also have posts in the Drupal StackExchange on opimizing MySQL

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For it worth : I"ve ran optimize table on the main tables of a database who works under heavy load. The main tables have been under great load of inserts/updates/deletes. The optimize reduced the table sizes by 90% and improved the system performance by more than twice !

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