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It seems like I will be needing transaction with MySQL and I have no idea how should I manage transactions in Mysql with mixed InnoDB/MyISAM tables, It all seems like a huge mess.
You might ask why would I ever want to mix the tables together… the anwer is PERFORMANCE. as many developers have noticed, InnoDB tables generally have bad performance, but in return give higher isolation level etc…
does anyone have any advice regarding this issue?
I think you are overrating the performance difference between MyISAM and InnoDB. MyISAM is faster in data warehousing situations (such as full table scan reporting, etc..), but InnoDB can actually be faster in many cases with normal OLTP queries.
InnoDB is harder to tune since it has more knobs, but a properly tuned InnoDB system can often have higher throughput than MyISAM due to better locking and better I/O patterns.