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What are the implications if I create all the Craft database tables on the InnoDB storage engine? Will there be any performance problem?

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Actually, all the tables, but one use InnoDB storage engine. The one that uses myisam engine is table "searchindex".

When you check for index type:

mysql> show index from searchindex where Index_type="FULLTEXT" \G

you get that the "searchindex" table indeed uses FULLTEXT.

I would say that Craft uses some specific fulltext searches specific to myisam engine, therefore not using innodb.

You can change the engine of the "searchindex" table (and see what brakes) with:

mysql> alter table searchindex engine="InnoDB";

and revert with:

alter table searchindex engine="MyISAM";
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