Description:
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The MYSQLI_OPT_READ_TIMEOUT option cannot be changed after a connection is established. This means if it is set to a low value to ensure a stable initial connection to the MySQL server, it cannot be raised back up again before executing long running queries.

Test script:
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<?php
$connection = mysqli_init();

//ensure we receive a reply from mysql in under 1 second
$connection->options(MYSQLI_OPT_READ_TIMEOUT, 1);

//connect to the mysql server
$connection->real_connect($server, $username, $password, $database);

//change timeout to 1 hour so we can run a long query
$connection->options(MYSQLI_OPT_READ_TIMEOUT, 60*60);

//attempt to pull results from a very large table, something that would exceed the initial 1 second timeout value, but not the 1 hour timeout value
$connection->query('SELECT * FROM `huge_table`');