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response time - Linux/Apache performance very slow even on local network

I have an Ubuntu server machine running Apache and MYSQL. System and version info is as follows:
Linux kernel 3.0.0.-12
Apache/2.2.20
MySQL Ver 14.14.Distrib 5.1.58



I am running a few websites on this server, some HTML only, some PHP/MySQL. THe [problem is that response time is very slow, both on static as well as the dynamic sites. Sometimes it takes more than 10 seconds before a response is given, this makes the sites very slow and almost unusable.
The problem occurs even when requesting from the local network. I have added the involved subdomains to my /etc/hosts file, and abolve all the problem is not solved by using IP numbers instead of URL's. So there is no DNS lookup issue.
I have modified the log format by showing the response times and sometimes a files takes 12 seconds to be served, see the jquery~.js file in the example screenshot.
I have no explanation for this extremely long response time, but is is not even the only issue here, some other files takes a long time to be served too, but do not show a long response time in the log file.
So probably different tissues are involved here. I cannot find a solution until now, any suggestions???
THanx in advance, Klaas



link to screenshot picture from access logfile




Some extra configuration info:



apache2.conf (comment is removed)



LockFile ${APACHE_LOCK_DIR}/accept.lock
PidFile ${APACHE_PID_FILE}
Timeout 300
KeepAlive On
MaxKeepAliveRequests 100

KeepAliveTimeout 5

StartServers 5
MinSpareServers 5
MaxSpareServers 10
MaxClients 150
MaxRequestsPerChild 0




StartServers 2
MinSpareThreads 25
MaxSpareThreads 75
ThreadLimit 64
ThreadsPerChild 25
MaxClients 150
MaxRequestsPerChild 0




StartServers 2
MinSpareThreads 25
MaxSpareThreads 75
ThreadLimit 64
ThreadsPerChild 25
MaxClients 150
MaxRequestsPerChild 0


User ${APACHE_RUN_USER}

Group ${APACHE_RUN_GROUP}

AccessFileName .htaccess


Order allow,deny
Deny from all
Satisfy all



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\" %T/%D" 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/


And the virtual hostfile for one of the slow sites, in fact it is pretty straightforward...





ServerAdmin blablabla@gmail.com
ServerSignature EMail
ServerName toenjoy.drsklaus.nl
DocumentRoot /var/www/toenjoy.drsklaus.nl

Options FollowSymLinks
AllowOverride None



Options Indexes FollowSymLinks MultiViews
AllowOverride AuthConfig
AuthType Basic
AuthName "To Enjoy"
AuthUserFile /etc/.htpasswd
Require user petraaa
Order allow,deny
allow from all



ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/

AllowOverride None
Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
Order allow,deny
Allow from all


ErrorLog /var/log/apache2/error.log


# Possible values include: debug, info, notice, warn, error, crit,
# alert, emerg.
LogLevel warn
CustomLog /var/log/apache2/access.log combined

Alias /doc/ "/usr/share/doc/"

Options Indexes MultiViews FollowSymLinks
AllowOverride None

Order deny,allow
Deny from all
Allow from 127.0.0.0/255.0.0.0 ::1/128




And the output of free -m:



klaas@ubuntu-server:/etc/apache2$ free -m

total used free shared buffers cached
Mem: 1997 1401 595 0 144 1017
-/+ buffers/cache: 238 1758
Swap: 2035 0 2035


and I have no indication that swapping occurs on the moments the site is slow.
I have runned top and it does not appear to be a CPU issue. I have the impression that the spawning of a apache thread could maybe be the bottleneck but it is just a suggestion.
Maybe this gives some extra information!




EDIT:
The problem seemed to be gone for some time but occurs again! And not only with Apache, also connecting using SSH takes a tremendous time, sometimes it takes up to 15 seconds before the keyphrase is asked for. Also scp works very slowly. The behavious is really unpredoctable and makes the server very hard to use.
Any ideas...?

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