The reason it takes time to consume is disk I / O speed. You can try using autoload, as you may need files that are not actually used. Another approach to reduce IO overhead on disk is to merge your PHP files into one large file. Requiring a large file that contains the code you always need is faster than including the same code in several small files.
In addition, APC has a function that speeds up the apc.include_once_override call, which you can try to enable.
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