Mysql high cpu usage (over 600%)

Question

The server has 8core CPU and 22 GB of ram. Every day receives many requests from users, and recently a replication mechanism has been activated, with an implementation of a db master and a slave. Now the server is really slow (on ssh top, mysqld reaches 600% and more of CPU Usage) and sometimes it go down of service. Please can you help me to fix this issue?

here is my mysql configuration file:

#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
# 
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

[mysqld_safe]
socket      = /var/run/mysqld/mysqld.sock
nice        = 0

[mysqld]
#
# * Basic Settings
#
user        = mysql
pid-file    = /var/run/mysqld/mysqld.pid
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /var/lib/mysql
tmpdir      = /tmp
lc-messages-dir = /usr/share/mysql
skip-external-locking
##
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
#bind-address       = 127.0.0.1
#
# * Fine Tuning
#
innodb_buffer_pool_size = 12G
key_buffer_size     = 1G
max_allowed_packet  = 256M
thread_stack        = 192K
thread_cache_size       = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover-options  = BACKUP
max_connections        = 300


#innodb_buffer_pool_instances=8
#innodb_read_io_threads=8
#innodb_write_io_threads=8

#open_files_limit = 1024
#table_open_cache = 400
server_id           = 2
bind-address        = 0.0.0.0
log_bin             = /var/log/mysql/mysql-bin.log
log_bin_index       = /var/log/mysql/mysql-bin.log.index
relay_log           = /var/log/mysql/mysql-relay-bin
relay_log_index     = /var/log/mysql/mysql-relay-bin.index
expire_logs_days    = 10
max_binlog_size     = 100M
log_slave_updates   = 1
auto-increment-increment = 2
auto-increment-offset = 2
replicate-ignore-db=phpmyadmin
replicate-ignore-db=mysql
skip-name-resolve
#table_cache            = 64
#thread_concurrency     = 10
#
# * Query Cache Configuration
#
query_cache_limit   = 0
query_cache_size        = 0

sort_buffer_size = 1M
join_buffer_size = 1M
read_buffer_size = 1M



#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1
#
# Error log - should be very few entries.
#
log_error = /var/log/mysql/error.log
#
# Here you can see queries with especially long duration
#log_slow_queries   = /var/log/mysql/mysql-slow.log
#long_query_time = 2
#log-queries-not-using-indexes
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
#       other settings you may need to change.
#server-id      = 1
#log_bin            = /var/log/mysql/mysql-bin.log
expire_logs_days    = 10
max_binlog_size   = 100M
#binlog_do_db       = include_database_name
#binlog_ignore_db   = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * Security Features
#
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem

Solution

Suggestions for your my.cnf [mysqld] section changes.

key_buffer_size=100M  # from 1G for more reasonable RAM allocation
thread_cache_size=100  # from 8 to reduce threads_created

REMOVE THE leading # from

innodb_buffer_pool_instances    for qty of 8 to minimize mutex contention

ADD

innodb_lru_scan_depth=100  # from 1024 default to reduce CPU cycles used every SECOND

REMOVE 4 leading # from innodb_read_io_threads and the next 3 # to activate these lines

innodb_read_io_threads=64  # from 8 to encourage multi core processing
innodb_write_io_threads=64  # from 8 to encourage multi core processing

open_files_limit=4096  # from 1024 for now
table_open_cache=2048  # from 400 for now

join_buffer_size=128K  # from 1M for more reasonable RAM per connection
read_buffer_size=128K  # from 1M for more reasonable RAM per connection 

the last one will reduce handler_read_next Rate Per Second significantly.