Incremental Backups in MySQL

Both xtrabackup and innobackupex tools supports incremental backups, which means that it can copy only the data that has changed since the last full backup. You can perform many incremental backups between each full backup, so you can set up a backup process such as a full backup once a week and an incremental backup every day, or full backups every day and incremental backups every hour.
Incremental backups work because each InnoDB page (usually 16kb in size) contains a log sequence number, or LSN. The LSN is the system version number for the entire database. Each page’s LSN shows how recently it was changed. An incremental backup copies each page whose LSN is newer than the previous incremental or full backup’s LSN. There are two algorithms in use to find the set of such pages to be copied. The first one, available with all the server types and versions, is to check the page LSN directly by reading all the data pages. The second one, available with Percona Server, is to enable the changed page tracking feature on the server, which will note the pages as they are being changed. This information will be then written out in a compact separate so-called bitmap file. The xtrabackup binary will use that file to read only the data pages it needs for the incremental backup, potentially saving many read requests. The latter algorithm is enabled by default if the xtrabackup binary finds the bitmap file. It is possible to specify --incremental-force-scan to read all the pages even if the bitmap data is available.
Incremental backups do not actually compare the data files to the previous backup’s data files. In fact, you can use --incremental-lsn to perform an incremental backup without even having the previous backup, if you know its LSN. Incremental backups simply read the pages and compare their LSN to the last backup’s LSN. You still need a full backup to recover the incremental changes, however; without a full backup to act as a base, the incremental backups are useless.

Creating an Incremental Backup

To make an incremental backup, begin with a full backup as usual. The xtrabackup binary writes a file called xtrabackup_checkpoints into the backup’s target directory. This file contains a line showing the to_lsn, which is the database’s LSN at the end of the backup. Create the full backup with a command such as the following:

xtrabackup --backup --target-dir=/data/backups/base --datadir=/var/lib/mysql/

If you want a usable full backup, use innobackupex since xtrabackup itself won’t copy table definitions, triggers, or anything else that’s not .ibd.
If you look at the xtrabackup_checkpoints file, you should see some contents similar to the following:

backup_type = full-backuped
from_lsn = 0
to_lsn = 1291135

Now that you have a full backup, you can make an incremental backup based on it. Use a command such as the following:

xtrabackup --backup --target-dir=/data/backups/inc1 \
--incremental-basedir=/data/backups/base --datadir=/var/lib/mysql/

The /data/backups/inc1/ directory should now contain delta files, such as ibdata1.delta and test/table1.ibd.delta. These represent the changes since the LSN 1291135. If you examine the xtrabackup_checkpoints file in this directory, you should see something similar to the following:

backup_type = incremental
from_lsn = 1291135
to_lsn = 1291340

The meaning should be self-evident. It’s now possible to use this directory as the base for yet another incremental backup:

xtrabackup --backup --target-dir=/data/backups/inc2 \
--incremental-basedir=/data/backups/inc1 --datadir=/var/lib/mysql/

Preparing the Incremental Backups

The --prepare step for incremental backups is not the same as for normal backups. In normal backups, two types of operations are performed to make the database consistent: committed transactions are replayed from the log file against the data files, and uncommitted transactions are rolled back. You must skip the rollback of uncommitted transactions when preparing a backup, because transactions that were uncommitted at the time of your backup may be in progress, and it’s likely that they will be committed in the next incremental backup. You should use the --apply-log-only option to prevent the rollback phase.
If you do not use the --apply-log-only option to prevent the rollback phase, then your incremental backups will be useless. After transactions have been rolled back, further incremental backups cannot be applied.
Beginning with the full backup you created, you can prepare it, and then apply the incremental differences to it. Recall that you have the following backups:

/data/backups/base
/data/backups/inc1
/data/backups/inc2

To prepare the base backup, you need to run --prepare as usual, but prevent the rollback phase:

xtrabackup --prepare --apply-log-only --target-dir=/data/backups/base

The output should end with some text such as the following:

101107 20:49:43  InnoDB: Shutdown completed; log sequence number 1291135

The log sequence number should match the to_lsn of the base backup, which you saw previously.
This backup is actually safe to restore as-is now, even though the rollback phase has been skipped. If you restore it and start MySQL, InnoDB will detect that the rollback phase was not performed, and it will do that in the background, as it usually does for a crash recovery upon start. It will notify you that the database was not shut down normally.
To apply the first incremental backup to the full backup, you should use the following command:

xtrabackup --prepare --apply-log-only --target-dir=/data/backups/base \
--incremental-dir=/data/backups/inc1

This applies the delta files to the files in /data/backups/base, which rolls them forward in time to the time of the incremental backup. It then applies the redo log as usual to the result. The final data is in /data/backups/base, not in the incremental directory. You should see some output such as the following:

incremental backup from 1291135 is enabled.
xtrabackup: cd to /data/backups/base/
xtrabackup: This target seems to be already prepared.
xtrabackup: xtrabackup_logfile detected: size=2097152, start_lsn=(1291340)
Applying /data/backups/inc1/ibdata1.delta ...
Applying /data/backups/inc1/test/table1.ibd.delta ...
.... snip
101107 20:56:30  InnoDB: Shutdown completed; log sequence number 1291340

Again, the LSN should match what you saw from your earlier inspection of the first incremental backup. If you restore the files from /data/backups/base, you should see the state of the database as of the first incremental backup.
Preparing the second incremental backup is a similar process: apply the deltas to the (modified) base backup, and you will roll its data forward in time to the point of the second incremental backup:

xtrabackup --prepare --target-dir=/data/backups/base \
--incremental-dir=/data/backups/inc2

Note

--apply-log-only should be used when merging all incrementals except the last one. That’s why the previous line doesn’t contain the --apply-log-only option. Even if the --apply-log-only was used on the last step, backup would still be consistent but in that case server would perform the rollback phase.

If you wish to avoid the notice that InnoDB was not shut down normally, when you have applied the desired deltas to the base backup, you can run --prepare again without disabling the rollback phase.