Apache CPU 100% when query DB - mysql

Question

I have an Ubuntu server and 10 sites with different framework / CMS.
My problem is that when I open a site with a big CMS integrated with MySQL DB, Apache2 using 100% CPU, in these sites I have a page speed between 10 - 20 seconds (to render HTML page) and I really don't know why. (but all PHP frameworks without a MySQL connection work fine).
With my server support manager we see all works well in my server (no I/O problem or others), and we think there is an issue in Apache / MySQL config.
I haven't crashed DB tables and optimized all innodb tables.
This is a top snapshot when I load this slow CMS from my browser:
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
13307 www-data 20 0 90116 42m 22m R 100 4.2 0:15.23 apache2
2224 root 20 0 37932 8148 1724 S 8 0.8 212:21.99 newrelic-daemon
13422 mysql 20 0 186m 47m 6280 S 0 4.7 0:11.20 mysqld
13889 root 20 0 2640 1132 860 R 0 0.1 0:00.03 top
1 root 20 0 2796 1124 792 S 0 0.1 0:06.28 init
Newrelic screenshot problem (not only with wordpress but all CMS): Newrelic screenshot
My CPU info:
$ head /proc/cpuinfo
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 45
model name : Intel(R) Xeon(R) CPU E5-2670 0 # 2.60GHz
stepping : 7
cpu MHz : 2600.086
cache size : 20480 KB
fdiv_bug : no
hlt_bug : no
My Memory info:
$ head /proc/meminfo
MemTotal: 1028476 kB
MemFree: 571424 kB
Buffers: 17920 kB
Cached: 273312 kB
SwapCached: 824 kB
Active: 232768 kB
Inactive: 180264 kB
Active(anon): 147336 kB
Inactive(anon): 5292 kB
Active(file): 85432 kB
My Apache Config:
LockFile ${APACHE_LOCK_DIR}/accept.lock
PidFile ${APACHE_PID_FILE}
Timeout 300
KeepAlive On
MaxKeepAliveRequests 100
KeepAliveTimeout 15
<IfModule mpm_prefork_module>
StartServers 2
MinSpareServers 5
MaxSpareServers 10
MaxClients 50
MaxRequestsPerChild 0
</IfModule>
<IfModule mpm_worker_module>
StartServers 2
MinSpareThreads 25
MaxSpareThreads 75
ThreadLimit 64
ThreadsPerChild 25
MaxClients 150
MaxRequestsPerChild 0
</IfModule>
<IfModule mpm_event_module>
StartServers 2
MinSpareThreads 5
MaxSpareThreads 10
ThreadLimit 64
ThreadsPerChild 25
MaxClients 50
MaxRequestsPerChild 0
</IfModule>
User ${APACHE_RUN_USER}
Group ${APACHE_RUN_GROUP}
AccessFileName .htaccess
<Files ~ "^\.ht">
Order allow,deny
Deny from all
Satisfy all
</Files>
DefaultType text/plain
HostnameLookups Off
ErrorLog ${APACHE_LOG_DIR}/error.log
LogLevel warn
Include mods-enabled/*.load
Include mods-enabled/*.conf
Include httpd.conf
Include ports.conf
LogFormat "%v:%p %h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" vhost_combined
LogFormat "%h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" combined
LogFormat "%h %l %u %t \"%r\" %>s %O" common
LogFormat "%{Referer}i -> %U" referer
LogFormat "%{User-agent}i" agent
Include conf.d/
Include sites-enabled/
MySQL Config:
[client]
port = 3306
socket = /var/run/mysqld/mysqld.sock
[mysqld_safe]
socket = /var/run/mysqld/mysqld.sock
nice = 0
[mysqld]
user = mysql
socket = /var/run/mysqld/mysqld.sock
port = 3306
basedir = /usr
datadir = /var/lib/mysql
tmpdir = /tmp
skip-external-locking
key_buffer = 32M
max_allowed_packet = 16M
thread_stack = 192K
thread_cache_size = 286
interactive_timeout = 25
wait_timeout = 1000
myisam-recover = BACKUP
myisam_sort_buffer_size = 32MB
max_connections = 400
read_buffer_size = 1M
sort_buffer_size = 2M
table_cache = 400
thread_concurrency = 10
query_cache_limit = 64M
query_cache_size = 32M
general_log_file = /var/log/mysql/mysql.log
log_error = /var/log/mysql/error.log
log_slow_queries = /var/log/mysql/mysql-slow.log
long_query_time = 4
log-queries-not-using-indexes
log_bin = /var/log/mysql/mysql-bin.log
expire_logs_days = 10
max_binlog_size = 100M
bind-address = 127.0.0.1
[mysqldump]
quick
quote-names
max_allowed_packet = 16M
[mysql]
[isamchk]
key_buffer = 32M
!includedir /etc/mysql/conf.d/
How to solve the issue?

Answer 1

There's a whole lot wrong with your Apache config - but that's probably irrelevant to the problem you are currently having, as is the state of your DBMS - based on the information you provided it's apache where things are going wrong.
You've no told us which MPM Apache is using (which is critical to understanding the problem) nor which CMS.
The information I've said you've omitted is just the tip of te iceberg - investigating and resolving performance issues is really, really complex - it can take months (much of which is spent gathering information) - you're very unlikely to get a definitive answer here.

Answer 2

You need to place more info. For example, if you try to display in wordpress 1000000 of posts and especially if you get properties of this posts in separate querys, you can get 100% CPU Usage for a big time.
Try to find a script, that cause this problem, montor your mysql (show processlist) in high usage moment and others.