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Does MySQL still ship the mysqlhotcopy script with its distro? You could use that for faster backup. If memory serves, it goes through each table doing a lock/flush/copy/unlock cycle.
It's only for MyISAM. You may ask yourself "but how does that handle cross-table dependencies"? The answer...it doesn't, because MyISAM ignores foreign keys anyway.
Ah, MySQL...
use Percona XtraBackup (http://www.percona.com/software/percona-xtrabackup/) for hotcopy
You would think the lack of innovation in MySQL over the years would of caused a shift towards something a little more resilient. Some of the biggest companies have used it, so yes it does scale, but it can require a lot of work such as setting up replication so you have a backup server.
You can use mysql replication, that would keep both databases in sync in realtime.
PM me with your email address and I can send you some documentation on setting up a replicating MySQL configuration.
Sadly I think now that Oracle owns it, MySQL won't ever become as awesome as it could have.
Oracle may not innovate MySQL that much, but they have increased the speed of MySQL Clustering in the latest release by a factor or 70, by fixing many outstanding bugs and a little refactoring. Not Bad!!
Still not many of us guys use a cluster with our VPSs