Going to one of my websites produces this;
Seconds later all goes back to normal again..... do I maybe have some sort of aggressive http logger or something installed?
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You have a problem with the PHP application running on your server.
Don't ask "which problem". You provide no information so we can't do also.
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How should we know what you have installed? Your package listing tells nothing about what gets executed when you receive an HTTP request.
It's run as a CGI, which is about the slowest method possible to run a script, but beyond that it might just be a really crappy PHP script or something that is inherently resource-hungry. Or one of countless other potential problems.