InnoDB is the default transactional storage engine for MySQL and the most important and broadly useful engine overall. It was designed for processing many short-lived transactions that usually complete rather than being rolled back. Its performance and automatic crash recovery make it popular for nontransactional storage needs, too. You should use InnoDB for your tables unless you have a compelling need to use a different engine.
MySQL uses a number of different independently developed storage engines. Whatever storage engine is used is dependent on use case.
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