MySQL Performance Issues

Question

Over the past 3 weeks we have been having bottle-necking issues at our MySQL server. I have been using MonYOG to watch the processlist in an attempt to get a grasp on the issues. We are aware that some of the queries and processes we are running in our code is less than optimized, but I am not completely convinced that is the main source of our issues. I feel our server should be able to overcome these issues.

Our tables are a mix of innodb and myISAM. I am by no means a DBA and do not pretend to be one so I am not sure what engine is the best in our current environment. We are pretty read heavy, but mix in a great deal of updates and inserts as well. I was seeing a lot of locked tables which made me think innodb might be better since it does row lock instead of table lock. I converted a few of our tables from MyISAM over to innodb to take advantage of some of the settings that are available. The developers are using a great deal of complex joins as well.

Here is what we are running in our my.cnf:

[mysqld]
datadir=/var/lib/mysql
port=3306
socket=/var/lib/mysql/mysql.sock
user=mysql

key_buffer_size=512M

innodb_file_per_table
innodb_buffer_pool_size=6GB
#the following line is causing some odd errors when doing db dump
#innodb_log_file_size=128M
innodb_log_buffer_size=8M
innodb_additional_mem_pool_size=32M

max_allowed_packet=16M
join_buffer_size=8M
sort_buffer_size=8M
max_connections=500
wait_timeout=500
skip-name-resolve
thread_cache=256
table_cache=256
tmp_table_size=48M
max_heap_table_size=48M

query_cache_size=64M

#logging of slow queries
log-slow-queries=/var/log/mysql-slow-query.log

# Default to using old password format for compatibility with mysql 3.x
# clients (those using the mysqlclient10 compatibility package).
#old_passwords=1

# Disabling symbolic-links is recommended to prevent assorted security risks;
# to do so, uncomment this line:
# symbolic-links=0

[mysqld_safe]
log-error=/var/log/mysqld.log
#pid-file=/var/run/mysqld/mysqld.pid

I changed the current "innodb_buffer_pool_size" to 6GB last week and that made a huge improvement to the bottle-necking. We have actually only really started seeing issues again today. Traffic has increased this week since we have schools starting and football season starting as well.

I have all kinds of statistical information I can supply you if needed. I am not sure what else to supply at this time.

If I cannot get this figured out I will be forced to call in a consultant. I am hoping someone will be able to give me a hand with some of these settings.

Thanks in advance.

------------------ EDIT--------------------

Here is some additional information requested:

MySQL Version - 5.0.95
OS version - CentOS 5.6 (will be upgrading to 6.4 in the coming weeks)

Server - Dell PowerEdge R710
CPU - Dual Quad Core 2.8GHz
RAM - 12GB
This is a dedicated machine. The only thing running on this box is MySQL