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After doing some research I heard only PHP 5.3.6+ supports PDO and SSL. I am not sure the validity of this, so I thought I would ask, and see if anyone has some suggestions for using PDO and transferring data between 2 mysql servers. It does not necessarily have to be SSL. Any form of encryption using a manually set key could work, I am just not sure where to begin. Thanks!

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You don't need PDO to have two MySQL servers talk to each other. Using replication and federated tables, you can do it directly without involving another layer. And that linkage can take place over an SSL connection as well.

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So what your saying is I can just set this up on both mysql servers and the connection by default will be encrypted and I do not have to worry about this on the PDO end?
No, not by default. You need to specify SSL options and certificates on both ends. PDO would only get involved if you're connecting to one of the servers to do queries. Otherwise any replication will take place purely between the two servers.
Ah, the problem is I do not want to completely sync the 2 databases. I just want the connection to be secure when I do mysql commands remotely to a server.
Ah. You didn't say it was for server usage, just intra-server communications. Check this comment on the PHP site: php.net/manual/en/ref.pdo-mysql.php#103501

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