Backup and Recovery

Backups are a very crucial part of any database setup. They are generally a copy of the data that can be used to reconstruct the data in case of any major or minor crisis with the database. In general terms, backups can be of two types:

Physical Backup - the data directory as it is on the disk
Logical Backup - the table structure and records in it

Both the above kinds of backups are supported by MySQL with different tools. It is the job of the SRE to identify which should be used when.

Mysqldump

This utility is available with MySQL installation. It helps in getting the logical backup of the database. It outputs a set of SQL statements to reconstruct the data. It is not recommended to use mysqldump for large tables as it might take a lot of time and the file size will be huge. However, for small tables it is the best and the quickest option.

mysqldump [options] > dump_output.sql

There are certain options that can be used with mysqldump to get an appropriate dump of the database.

To dump all the databases:

mysqldump -u<user> -p<pwd> --all-databases > all_dbs.sql

To dump specific databases:

mysqldump -u<user> -p<pwd> --databases db1 db2 db3 > dbs.sql

To dump a single database:

mysqldump -u<user> -p<pwd> --databases db1 > db1.sql

OR

mysqldump -u<user> -p<pwd> db1 > db1.sql

The difference between the above two commands is that the latter one does not contain the CREATE DATABASE command in the backup output.

To dump specific tables in a database:

mysqldump -u<user> -p<pwd> db1 table1 table2 > db1_tables.sql

To dump only table structures and no data:

mysqldump -u<user> -p<pwd> --no-data db1 > db1_structure.sql

To dump only table data and no CREATE statements:

mysqldump -u<user> -p<pwd> --no-create-info db1 > db1_data.sql

To dump only specific records from a table:

mysqldump -u<user> -p<pwd> --no-create-info db1 table1 --where=”salary>80000” > db1_table1_80000.sql

mysqldump can also provide output in CSV, other delimited text or XML format to support use-cases if any. The backup from mysqldump utility is offline, i.e. when the backup finishes it will not have the changes to the database which were made when the backup was going on. For example, if the backup started at 3:00 pm and finished at 4:00 pm, it will not have the changes made to the database between 3:00 and 4:00 pm.

Restoring from mysqldump can be done in the following two ways:

From shell

mysql -u<user> -p<pwd> < all_dbs.sql

OR

From shell, if the database is already created:

mysql -u<user> -p<pwd> db1 < db1.sql

From within MySQL shell:

mysql> source all_dbs.sql

Percona XtraBackup

This utility is installed separately from the MySQL server and is open source, provided by Percona. It helps in getting the full or partial physical backup of the database. It provides online backup of the database, i.e. it will have the changes made to the database when the backup was going on as explained at the end of the previous section.

Full Backup - the complete backup of the database.
Partial Backup - Incremental
Cumulative - After one full backup, the next backups will have changes post the full backup. For example, we took a full backup on Sunday, from Monday onwards every backup will have changes after Sunday; so, Tuesday’s backup will have Monday’s changes as well, Wednesday’s backup will have changes of Monday and Tuesday as well and so on.
Differential - After one full backup, the next backups will have changes post the previous incremental backup. For example, we took a full backup on Sunday, Monday will have changes done after Sunday, Tuesday will have changes done after Monday, and so on.

partial backups - differential and cummulative

Percona XtraBackup allows us to get both full and incremental backups as we desire. However, incremental backups take less space than a full backup (if taken per day) but the restore time of incremental backups is more than that of full backups.

Creating a full backup

xtrabackup --defaults-file=<location to my.cnf> --user=<mysql user> --password=<mysql password> --backup --target-dir=<location of target directory>

Example:

xtrabackup --defaults-file=/etc/my.cnf --user=some_user --password=XXXX --backup --target-dir=/mnt/data/backup/

Some other options

--stream - can be used to stream the backup files to standard output in a specified format. xbstream is the only option for now.
--tmp-dir - set this to a tmp directory to be used for temporary files while taking backups.
--parallel - set this to the number of threads that can be used to parallely copy data files to target directory.
--compress - by default - quicklz is used. Set this to have the backup in compressed format. Each file is a .qp compressed file and can be extracted by qpress file archiver.
--decompress - decompresses all the files which were compressed with the .qp extension. It will not delete the .qp files after decompression. To do that, use --remove-original along with this. Please note that the decompress option should be run separately from the xtrabackup command that used the compress option.

Preparing a backup

Once the backup is done with the --backup option, we need to prepare it in order to restore it. This is done to make the data files consistent with point-in-time. There might have been some transactions going on while the backup was being executed and those have changed the data files. When we prepare a backup, all those transactions are applied to the data files.

xtrabackup --prepare --target-dir=<where backup is taken>

Example:

xtrabackup --prepare --target-dir=/mnt/data/backup/

It is not recommended to halt a process which is preparing the backup as that might cause data file corruption and backup cannot be used further. The backup will have to be taken again.

Restoring a Full Backup

To restore the backup which is created and prepared from above commands, just copy everything from the backup target-dir to the data-dir of MySQL server, change the ownership of all files to MySQL user (the Linux user used by MySQL server) and start MySQL.

Or the below command can be used as well,

xtrabackup --defaults-file=/etc/my.cnf --copy-back --target-dir=/mnt/data/backups/

Note - the backup has to be prepared in order to restore it.

Creating Incremental backups

Percona XtraBackup helps create incremental backups, i.e, only the changes can be backed up since the last backup. Every InnoDB page contains a log sequence number or LSN that is also mentioned as one of the last lines of backup and prepare commands.

xtrabackup: Transaction log of lsn <LSN> to <LSN> was copied.

OR

InnoDB: Shutdown completed; log sequence number <LSN>
<timestamp> completed OK!

This indicates that the backup has been taken till the log sequence number mentioned. This is a key information in understanding incremental backups and working towards automating one. Incremental backups do not compare data files for changes, instead, they go through the InnoDB pages and compare their LSN to the last backup’s LSN. So, without one full backup, the incremental backups are useless.

The xtrabackup command creates a xtrabackup_checkpoint file which has the information about the LSN of the backup. Below are the key contents of the file:

backup_type = full-backuped | incremental
from_lsn = 0 (full backup) | to_lsn of last backup <LSN>
to_lsn = <LSN>
last_lsn = <LSN>

There is a difference between to_lsn and last_lsn. When the last_lsn is more than to_lsn that means there are transactions that ran while we took the backup and are yet to be applied. That is what --prepare is used for.

To take incremental backups, first, we require one full backup.

xtrabackup --defaults-file=/etc/my.cnf --user=some_user --password=XXXX --backup --target-dir=/mnt/data/backup/full/

Let’s assume the contents of the xtrabackup_checkpoint file to be as follows:

backup_type = full-backuped
from_lsn = 0
to_lsn = 1000
last_lsn = 1000

Now that we have one full backup, we can have an incremental backup that takes the changes. We will go with differential incremental backups.

xtrabackup --defaults-file=/etc/my.cnf --user=some_user --password=XXXX --backup --target-dir=/mnt/data/backup/incr1/ --incremental-basedir=/mnt/data/backup/full/

There are delta files created in the incr1 directory like, ibdata1.delta, db1/tbl1.ibd.delta with the changes from the full directory. The xtrabackup_checkpoint file will thus have the following contents.

backup_type = incremental
from_lsn = 1000
to_lsn = 1500
last_lsn = 1500

Hence, the from_lsn here is equal to the to_lsn of the last backup or the basedir provided for the incremental backups. For the next incremental backup, we can use this incremental backup as the basedir.

xtrabackup --defaults-file=/etc/my.cnf --user=some_user --password=XXXX --backup --target-dir=/mnt/data/backup/incr2/ --incremental-basedir=/mnt/data/backup/incr1/

The xtrabackup_checkpoint file will thus have the following contents:

backup_type = incremental
from_lsn = 1500
to_lsn = 2000
last_lsn = 2200

Preparing Incremental backups

Preparing incremental backups is not the same as preparing a full backup. When prepare runs, two operations are performed - committed transactions are applied on the data files and uncommitted transactions are rolled back. While preparing incremental backups, we have to skip rollback of uncommitted transactions as it is likely that they might get committed in the next incremental backup. If we rollback uncommitted transactions, the further incremental backups cannot be applied.

We use --apply-log-only option along with --prepare to avoid the rollback phase.

From the last section, we had the following directories with complete backup:

/mnt/data/backup/full
/mnt/data/backup/incr1
/mnt/data/backup/incr2

First, we prepare the full backup, but only with the --apply-log-only option.

xtrabackup --prepare --apply-log-only --target-dir=/mnt/data/backup/full

The output of the command will contain the following at the end.

InnoDB: Shutdown complete; log sequence number 1000
<timestamp> Completed OK!

Note the LSN mentioned at the end is the same as the to_lsn from the xtrabackup_checkpoint created for full backup.

Next, we apply the changes from the first incremental backup to the full backup.

xtrabackup --prepare --apply-log-only --target-dir=/mnt/data/backup/full --incremental-dir=/mnt/data/backup/incr1

This applies the delta files in the incremental directory to the full backup directory. It rolls the data files in the full backup directory forward to the time of incremental backup and applies the redo logs as usual.

Lastly, we apply the last incremental backup same as the previous one with just a small change.

xtrabackup --prepare --target-dir=/mnt/data/backup/full --incremental-dir=/mnt/data/backup/incr1

We do not have to use the --apply-log-only option with it. It applies the incr2 delta files to the full backup data files taking them forward, applies redo logs on them and finally rollbacks the uncommitted transactions to produce the final result. The data now present in the full backup directory can now be used to restore.

Note: To create cumulative incremental backups, the incremental-basedir should always be the full backup directory for every incremental backup. While preparing, we can start with the full backup with the --apply-log-only option and use just the last incremental backup for the final --prepare as that has all the changes since the full backup.

Restoring Incremental backups

Once all the above steps are completed, restoring is the same as done for a full backup.

Backup and Recovery