Is it better to separate your MySQL server and web server to two physical machines?

Separation is not necessarily better or worse. It’s a choice based on your individual circumstances. Since not separating them is administratively easier, it may be best to start this way. If you then see slowness arise due to too many TCP connections, consider options to fix it. One option is to just increase the number of TCP connections on the box. If this is not an option for you, physical separation (putting MySQL server and web server on different boxes) may now be the best thing.

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