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We have developed a Facebook application... we launched and had over a thousand users in 12 mins. The problem is the application did not handle it and so we had to take it back offline. Where should we start to analyse it? It is PHP based with a MySQL database.

What tools can I use to find where and what was causing the slow down?

The server is dedicated linux with 4gig of ram and a core2duo chip.

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A Facebook application functions much like a regular website. All the same optimization techniques apply so look for other questions on website performance that include web server (apache, nginx, etc.), PHP optimizations, use of caching, database optimizations, etc. etc.

For Facebook apps there's a performance guide:

And Facebook developed XHProf to help identify performance bottlenecks:

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