Mysql – Joins performed without indexes: 5568

You have a server with 256M, but you can't use all of that -- remember there's some OS overhead. Add to that with the fact you're over committing as other folks have mentioned and you'll definitely thrash here. 256M is only enough for a small DB, 20 connections is a lot with what you've got configured.

1) reduce your max connections to 4 (you're using 3 out of 20)

2) optimize your query cache better; 8M is really large, and 64M total is a lot based on your hits/prunes; try a 4/32 combo and see how it goes. Really I think a 2/24 combo would work for you.

3) you have no sorts requiring temp tables, why is that max_heap_table_size verb in there? Comment that out, use the defaults

4) do you actually have 128 tables? Try cutting that table_cache in half to 64 or 48

5) reduce thread_cache_size to 4

6) optimize those tables to reduce fragmenting

Those are some things to start with. It looks like you threw a bunch of numbers in a config without any actual profiling to know what you needed and have created a mess; if all else fails go back to the defaults and get rid of your custom settings and start over using some performance tuning guides you can find on Google. Get the output of SHOW VARIABLES and SHOW STATUS, find any one of a bajillion tuning guides and plug in your actual, real numbers into their equations and that'll tell you the exact-ish numbers you need to put in your config file.

Are your InnoDB Log Files (ib_logfile0 and ib_logfile1) sized correctly ?

They should be 25% of the InnoDB Buffer Pool
In your case, that would be 224M

You can it them as follows:

1. Add this setting to /etc/my.cnf : innodb_log_file_size=224M
2. service mysql stop
3. rm -f /var/lib/mysql/ib_logfile[01]
4. service mysql start (ib_logfile0 and ib_logfile1 are recreated)

You should keep the default for innodb_flush_method to insure ACID compliance. Otherwise, you could lose up to one second's worth of transactions.

CAVEAT: If your DB server is dedicated to only to the database, you should reserve 75-80% or RAM for the innodb_buffer_pool.

UPDATE

You will definitely want to change your InnoDB layout !!!!

You need to raise innodb_open_files to 6000
You need to turn on innodb_file_per_table
You need to restructure all InnoDB Data to reside in separate tablespaces