Server.php causing 100%CPU usage

Hi
I have a server with Centos 6.5 running ISPconfig 3 after following this guide
https://www.howtoforge.com/perfect-...l-php-pureftpd-postfix-dovecot-and-ispconfig3

there's an issue with php processes running and taking up 100% cpu, eventually taking up 100% memory too and causing the server to crash.
if I run htop I see lots of these....
/usr/bin/php -q /usr/local/ispconfig/server/server.php

any idea how to check whats causing this?

 

ok, so I turned on "Debug" log levels and got a message saying...
There is already an instance of server.php running. Exiting.

Then I follow these steps
1) Comment out the server.sh cronjob in the root crontab.
2) Delete the lockfile:
rm -f /usr/local/ispconfig/server/temp/.ispconfig_lock
3) run:
/usr/bin/php -q /usr/local/ispconfig/server/server.php

And now I'm getting this output...

# /usr/bin/php -q /usr/local/ispconfig/server/server.php
23.06.2015-04:44 - DEBUG - Set Lock: /usr/local/ispconfig/server/temp/.ispconfig_lock
23.06.2015-04:44 - DEBUG - Found 28 changes, starting update process.
23.06.2015-04:44 - DEBUG - Calling function 'ssl' from plugin 'apache2_plugin' raised by event 'web_domain_update'.
23.06.2015-04:44 - DEBUG - Calling function 'update' from plugin 'apache2_plugin' raised by event 'web_domain_update'.
PHP Warning: escapeshellcmd() has been disabled for security reasons in /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php on line 408
PHP Warning: escapeshellcmd() has been disabled for security reasons in /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php on line 415
PHP Warning: escapeshellcmd() has been disabled for security reasons in /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php on line 418
PHP Warning: exec() has been disabled for security reasons in /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php on line 418
23.06.2015-04:44 - DEBUG - Adding the user:
PHP Warning: escapeshellcmd() has been disabled for security reasons in /usr/local/ispconfig/server/lib/classes/system.inc.php on line 1605
PHP Warning: exec() has been disabled for security reasons in /usr/local/ispconfig/server/lib/classes/system.inc.php on line 1605
PHP Warning: exec() has been disabled for security reasons in /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php on line 559
PHP Warning: escapeshellarg() has been disabled for security reasons in /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php on line 564
PHP Warning: escapeshellarg() has been disabled for security reasons in /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php on line 564
PHP Warning: exec() has been disabled for security reasons in /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php on line 564
PHP Warning: escapeshellcmd() has been disabled for security reasons in /usr/local/ispconfig/server/lib/classes/system.inc.php on line 1602
PHP Warning: exec() has been disabled for security reasons in /usr/local/ispconfig/server/lib/classes/system.inc.php on line 1602
PHP Warning: escapeshellcmd() has been disabled for security reasons in /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php on line 611
PHP Warning: escapeshellcmd() has been disabled for security reasons in /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php on line 611
PHP Warning: touch(): Unable to create file because No such file or directory in /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php on line 2909


and if I run
# /usr/local/ispconfig/server/server.sh
I get the first message again...

23.06.2015-04:49 - DEBUG - There is already an instance of server.php running. Exiting.

 

I repeated these a few times
2) Delete the lockfile:
rm -f /usr/local/ispconfig/server/temp/.ispconfig_lock
3) run:
/usr/bin/php -q /usr/local/ispconfig/server/server.php

and it looks much better now but I'm still left with lots of processes running server.php.
/usr/bin/php -q /usr/local/ispconfig/server/server.php

is it safe to kill those off?