There are numerous reasons that your site could be running slowly. Of course there could always be hardware concerns. Your statement seems to indicate that the database and the web server are on the same box. Checking your hardware's performance logs could reveal problems.
Though there may be hardware issues I am going to guess that the performance issues are more likely to be a result of poor database and/or query optimization. First take a look at your database design and determine of you have followed the rules of normalization or normal form. Then have someone else take a look at your data model, it never hurts to get a second opinion. Remember you can nad should check up on the
health of your database as well.
If you have all your data normalized and modeled well take a look at your queries. With MySQL you can append the the
EXPLAIN statement to the front of a SELECT query to see how well it is running. If your SELECT queries are not searching indexes then you will be able to determine where you need indexes based on the information given. Be sure to read the
documentation topic about optimization.
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