CPU is about 332% mainly due to mysqld

Hello Community

I have a big problem with my MYSQL server eating up lifting the overload CPU of my server to about 332%.

In fact, I am hosted about 10 websites mainly for classifieds ads where the read/write are quite intense.

Please do see below my actual my.cnf 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.
[client]
port            = 3306
socket          = /var/run/mysqld/mysqld.sock

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

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket          = /var/run/mysqld/mysqld.sock
nice            = 0

[mysqld]

key_buffer = 292M
sort_buffer_size = 4M
read_buffer_size = 4M
read_rnd_buffer_size = 4M
myisam_sort_buffer_size = 16M
query_cache_size = 56M

#
# * 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
#
#key_buffer             = 16M
max_allowed_packet      = 16M
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         = BACKUP
#max_connections        = 100
#table_cache            = 64
#thread_concurrency     = 10
#
# * Query Cache Configuration
#
query_cache_limit       = 1M
#query_cache_size        = 16M
#
# * 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

[mysqldump]
quick
quote-names
max_allowed_packet      = 16M

[mysql]
#no-auto-rehash # faster start of mysql but no tab completition

[isamchk]
key_buffer              = 16M

#
# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/

And this is the actual free -m

> root@xxxxx:~# free -m

total used free shared buffers cached

Mem: 7950 3000 4950 0 105 1679

-/+ buffers/cache: 1215 6735

Swap: 255 0 255

And this is the actual ps -eo pmem,pcpu,rss,vsize,args | sort -k 1 -r | less

%MEM %CPU   RSS    VSZ COMMAND
 4.8  271 395536 4895732 /usr/sbin/mysqld
 2.8  0.1 233952 511892 /usr/sbin/clamd
 1.1  0.0 93764 216596 amavisd (ch6-avail)
 1.1  0.0 93756 216596 amavisd (ch6-avail)
 1.1  0.0 90816 212572 amavisd (master)
 0.8  4.4 69040 389180 /usr/bin/memcached -m 64 -p 11211 -u memcache -l 127.0.0.1
 0.6  0.0 56588 140576 /usr/sbin/spamd --create-prefs --max-children 5 --helper-home-dir -d --pidfile=/var/run/spamd.pid
 0.6  0.0 54156 140576 spamd child
 0.6  0.0 54156 140576 spamd child
 0.2  7.3 17188 308924 /usr/sbin/apache2 -k start
 0.2  6.5 20764 310104 /usr/sbin/apache2 -k start
 0.2  5.6 18572 310136 /usr/sbin/apache2 -k start
 0.2  5.5 19476 310648 /usr/sbin/apache2 -k start
 0.2  5.3 18388 309848 /usr/sbin/apache2 -k start
 0.2  5.1 21820 312256 /usr/sbin/apache2 -k start
 0.2  4.9 19372 308428 /usr/sbin/apache2 -k start
 0.2  4.8 17964 308848 /usr/sbin/apache2 -k start
 0.2  4.8 17032 308056 /usr/sbin/apache2 -k start
 0.2  4.7 17856 309272 /usr/sbin/apache2 -k start
 0.2  4.6 16988 308848 /usr/sbin/apache2 -k start
 0.2  4.4 23636 314872 /usr/sbin/apache2 -k start
 0.2  4.4 19924 310908 /usr/sbin/apache2 -k start
 0.2  4.3 19500 310760 /usr/sbin/apache2 -k start
 0.2  4.1 20328 311036 /usr/sbin/apache2 -k start
 0.2  4.0 19412 308416 /usr/sbin/apache2 -k start
 0.2  3.9 19208 308316 /usr/sbin/apache2 -k start
 0.2  3.6 19404 310480 /usr/sbin/apache2 -k start
 0.2  2.6 20772 314016 /usr/sbin/apache2 -k start
 0.2 16.7 17524 309592 /usr/sbin/apache2 -k start
 0.2 14.7 17748 308824 /usr/sbin/apache2 -k start
 0.2 10.4 16976 309336 /usr/sbin/apache2 -k start
 0.2  0.2 21584  86940 linode-longview
 0.2  0.0 22140  85688 /usr/bin/perl /usr/share/webmin/miniserv.pl /etc/webmin/miniserv.conf
 0.1  9.5 16268 308420 /usr/sbin/apache2 -k start
 0.1  0.2 11664 306444 /usr/sbin/apache2 -k start
 0.0  5.5     0      0 [rcu_sched]
 0.0  2.8     0      0 [apache2] <defunct>0.0  2.1  5544  19448 find /var/lib/php5/ -depth -mindepth 1 -maxdepth 1 -type f -cmin +24 ! -execdir fuser -s {} ; -delete
 0.0  1.5  1524 249476 rsyslogd -c5
 0.0  0.6  4132  22896 -bash
 0.0  0.2  6004 482044 /usr/sbin/opendkim -x /etc/opendkim.conf -u opendkim -P /var/run/opendkim/opendkim.pid -p inet:8891@localhost
 0.0  0.2  5456 133672 smtpd -n smtp -t inet -u -c -o stress= -s 2 -v
 0.0  0.2  5404 133580 smtpd -n smtp -t inet -u -c -o stress= -s 2 -v
 0.0  0.2  5388 133580 smtpd -n smtp -t inet -u -c -o stress= -s 2 -v
 0.0  0.2  1956  39840 /usr/bin/freshclam -d --quiet
 0.0  0.2  1676  25112 /usr/lib/postfix/master
 0.0  0.1  5424 133580 smtpd -n smtp -t inet -u -c -o stress= -s 2 -v
 0.0  0.1  2588 115848 trivial-rewrite -n rewrite -t unix -u -c
 0.0  0.1     0      0 [ksoftirqd/7]
 0.0  0.1     0      0 [ksoftirqd/5]
 0.0  0.1     0      0 [ksoftirqd/4]
 0.0  0.1     0      0 [ksoftirqd/3]
 0.0  0.1     0      0 [ksoftirqd/2]
 0.0  0.1     0      0 [ksoftirqd/1]
 0.0  0.1     0      0 [kjournald]
 0.0  0.0   916   8956 dovecot/anvil
 0.0  0.0   868  12756 /sbin/getty -8 38400 hvc0
 0.0  0.0   812   7176 fuser -s ./sess_edndcjrslr1bh4qje8g4aoi004
 0.0  0.0   792  21468 /sbin/udevd --daemon
:</defunct> 

Can someone please help on the best way to make ny server running properly? (By teh way, I am using 8Gb linode one)

Regards

Cloud Dreamer