Often the phpBB3 search functionality is abused by different spam bots. They perform searches as guest users.
This significantly increases the size of the search_wordmatch table. It contains pairs of data of which posts include which words from the search_wordlist table. Usually, when the table is large slow MySQL queries are generated.
As a solution you should disable the search functionality for guest users. This can be done from the phpBB3 admin panel->Users and Groups->Groups' permissions. Select Guests from the drop down menu and click on the Submit button. Click on the Advanced permissions link and then open the Misc tab. Set Never for the Can search board option and confirm the modification by clicking on the Apply permissions button.
Additionally, you can increase the User search flood interval and the Common word threshold values from the phpBB3 admin panel->General->Search settings.
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