When it comes to InnoDB, you are right to be concerned.
Here is a Pictorial Representation of InnoDB (Made by Percona CTO Vadim Tkachenko)
The whole left side of the diagram represents InnoDB's moving parts in memory. The critical piece here is the InnoDB Buffer Pool
The InnoDB Buffer Pool holds three things
- Data Pages : If a page is dirty, it is eventually written to its
- Index Pages : If a page is dirty, it is eventually written to its
- Secondary Index Changes : Dirty index pages related to non-unique indexes are written to ibdata1
Any page that has been updated is also written beforehand into the Double Write Buffer inside ibdata1.
If you rsync everything in datadir, you are chasing too many moving files
- ibdata1 itself has moving parts
- Double Write Buffer
- Inset buffer
- Rollback Segments
- Undo Logs
- Redo Logs (ib_logfile0 and ib_logfile1)
.ibd file being updated
If you had to rsync your datadir to back it up and you attempt to setup it and start mysql, the best case scenario would be crash recovery, an initiated repair of data and index pages using the Double Write Buffer and the Insert Buffer and some playback from the Redo Logs. This will roll forward whatever data can be saved via crash recovery.
It would be fair to say that rsync could possibly miss dirty pages that have not been written the Double Write Buffer and the Insert Buffer if the rsync got passed it already.
I have written posts about doing rsyncs for backup
If you want to try to rsync, you could use the script from How do I replicate a MySql server's data without using mysqldump? but you need to properly flush all moving parts
About 10 minutes before the backup, set buffer pool to have dirty pages flush aggregsively
SET GLOBAL innodb_max_dirty_pages_pct = 0;
Then, just before starting the rsync, run these commands
FLUSH TABLES WITH READ LOCK;
SELECT CONNECTION_ID() ID_With_Lock;
You could run the rsync at this point, but any new transaction will be held up in the Buffer Pool and will not commit to disk until you login to MySQL in a separate session and kill the process ID (ID_With_Lock).
It is possible to have a good rsync backup if handled with great care. Percona XtraDB Cluster has 3 modes of adding new node to a Galera Cluster (xtrabackup, mysqldump, rsync)
If you are not that confident doing rsync backups, you are better off just doing
mysqldump --single-transacton and retrieving binlog events to copy data and roll forward to what ever point-in-time you want. You could also resort to Percona XtraBackup and let it do the heavy lifting.