Mysql – Setting MySQL slow query to less than 1 second

You have to use InnoDB. Here is why :

The major advantages of InnoDB over MyISAM

• InnoDB caches data and index pages, whereas MyISAM only caches index pages.
• InnoDB is designed for ACID-compliant transactions
• InnoDB is designed for row-level locking, MyISAM uses table-level locking.
• InnoDB is designed for Multiversion Concurrency Control, critical for transaction isolation
• InnoDB can be tuned to engage multiple cores

MyISAM is great in a read-heavy environment. Although you can configre private caches on a per-table basis, MyISAM never caches data.

InnoDB is your best bet !!!

CAVEAT

Get enough RAM on the DB Server to cache everything in the InnoDB Buffer Pool (75% of Installed RAM).

As you are saying that most of the tables are MyISAM, I would check IOs and locking.

You can verify you disk throughput with a tool like iotop.

http://www.manpagez.com/man/1/iotop/

MyISAM relies on the file system cache to store data blocks, so MySQL has to compete with all the other processes running on your OS for access to that cache. The key_buffer only applies to index blocks.

http://dev.mysql.com/doc/refman/5.0/en/myisam-key-cache.html

If you notice that MySQL is generating a lot of IO activity, that may mean that your OS is starved for RAM in spite of the 16GB you say is available.

I ran into a similar problem with a Wordpress install lately that relied heavily on two 2GB MySIAM tables.

If your SELECT statements are trying to access data from these same tables that are being modified at the same time by (DML) INSERT, UPDATE or DELETE queries, that might explain why table_locks_waited is so high on your system. Those DML queries could be coming from a website, a cron job or some other process. If locking contention is the problem, you may want to consider converting the table engine to InnoDB for those tables that are causing the most locking. Tools like Jet Profiler and Innotop can help you to get that specific information.