How To Configure MySQL Backups with Percona XtraBackup on Ubuntu 16.04

How To Configure MySQL Backups with Percona XtraBackup on Ubuntu 16.04


Databases often store some of the most valuable information in your infrastructure. Because of this, it is important to have reliable backups to guard against data loss in the event of an accident or hardware failure.

The Percona XtraBackup backup tools provide a method of performing “hot” backups of MySQL data while the system is running. They do this by copying the data files at the filesystem level and then performing a crash recovery to achieve consistency within the dataset.

In this guide, we will create a system to automate backups of MySQL data on an Ubuntu 16.04 server. We will use cron and the Percona tools in a group of scripts to create regular, secure backups that we can use for recovery in case of problems.


To complete this guide, you will need an Ubuntu 16.04 server with a non-root sudo user configured for administrative tasks. You can follow our “Initial Server Setup with Ubuntu 16.04” guide to set up a user with these privileges on your server.

Once you have a sudo user available, you will need to install MySQL. Either of these guides can be used, depending on which package you would like to use. The first guide is appropriate if you want to stick with the official Ubuntu repositories, while the second guide is better suited if you require more up-to-date features:

Once MySQL is installed, log into your server as your sudo user to continue.

Installing the Percona Xtrabackup Tools

The first thing we need to do is install the actual Percona backup utilities. The project maintains its own repositories that we can add to our MySQL server to gain access to the packages.

To start, go to the Percona release page for Ubuntu to find the latest .deb packages for installing the repository. Since we are on Ubuntu 16.04, which is codenamed “Xenial Xerus”, we should choose the “xenial” package. Right-click the corresponding link and copy the address.

Note: You can double-check the release codename of your server at any time by typing:

  1. lsb_release -c
Codename: xenial

Once you have copied the link, move to the /tmp directory and then download the repository configuration package with curl:

  1. cd /tmp
  2. curl -LO https://repo.percona.com/apt/percona-release_0.1-4.xenial_all.deb

Next, use dpkg to install the downloaded package, which will configure the Percona apt repository on the system:

  1. sudo dpkg -i percona*

With the new repository configured, we’ll update the local package index to pull down information about the newly available packages. We will then install the XtraBackup tools and the qpress compression utility from the repository:

  1. sudo apt-get update
  2. sudo apt-get install percona-xtrabackup-24 qpress

Among other bundled utilities, the xtrabackup, xbstream, and qpress commands will now be available. Our scripts will use each of these to perform backups and restore data.

Configuring a MySQL Backup User and Adding Test Data

To begin, start up an interactive MySQL session with the MySQL root user:

  1. mysql -u root -p

You will be prompted for the administrative password you selected during the MySQL installation. Once you’ve entered the password, you will be dropped into a MySQL session.

Create a MySQL User with Appropriate Privileges

The first thing we need to do is create a new MySQL user configured to handle backup tasks. We will only give this user the privileges it needs to copy the data safely while the system is running.

To be explicit about the account’s purpose, we will call the new user backup. We will be placing the user’s credentials in a secure file, so feel free to choose a complex password:

  1. CREATE USER 'backup'@'localhost' IDENTIFIED BY 'password';

Next we need to grant the new backup user the permissions it needs to perform all backup actions on the database system. Grant the required privileges and apply them to the current session by typing:


Our MySQL backup user is configured and has the access it requires.

Create Test Data for the Backups

Next, we will create some test data. Run the following commands to create a playground database with an equipment table. We will start by inserting a single record representing a blue slide:

  1. CREATE DATABASE playground;
  2. CREATE TABLE playground.equipment ( id INT NOT NULL AUTO_INCREMENT, type VARCHAR(50), quant INT, color VARCHAR(25), PRIMARY KEY(id));
  3. INSERT INTO playground.equipment (type, quant, color) VALUES ("slide", 2, "blue");

Later in this guide, we will use and alter this data to test our ability to create full and incremental backups.

Before we end our MySQL session, we will check the value of the datadir variable. We will need to know this value to ensure that our system-level backup user has access to the MySQL data files.

Display the value of the datadir variable by typing:

  1. SELECT @@datadir;
+-----------------+ | @@datadir | +-----------------+ | /var/lib/mysql/ | +-----------------+ 1 row in set (0.01 sec)

Take a note of the location you find.

This is all that we need to do within MySQL at the moment. Exit to the shell by typing:

  1. exit

Next, we can take a look at some system-level configuration.

Configuring a Systems Backup User and Assigning Permissions

Now that we have a MySQL user to perform backups, we will ensure that a corresponding Linux user exists with similar limited privileges.

On Ubuntu 16.04, a backup user and corresponding backup group is already available. Confirm this by checking the /etc/passwd and /etc/group files with the following command:

  1. grep backup /etc/passwd /etc/group
/etc/passwd:backup:x:34:34:backup:/var/backups:/usr/sbin/nologin /etc/group:backup:x:34:

The first line from the /etc/passwd file describes the backup user, while the second line from the /etc/group file defines the backup group.

The /var/lib/mysql directory where the MySQL data is kept is owned by the mysql user and group. We can add the backup user to the mysql group to safely allow access to the database files and directories. We should also add our sudo user to the backup group so that we can access the files we will back up.

Type the following commands to add the backup user to the mysql group and your sudo user to the backup group:

  1. sudo usermod -aG mysql backup
  2. sudo usermod -aG backup ${USER}

If we check the /etc/group files again, you will see that your current user is added to the backup group and that the backup user is added to the mysql group:

  1. grep backup /etc/group
backup:x:34:sammy mysql:x:116:backup

The new group isn’t available in our current session automatically. To re-evaluate the groups available to our sudo user, either log out and log back in, or type:

  1. exec su - ${USER}

You will be prompted for your sudo user’s password to continue. Confirm that your current session now has access to the backup group by checking our user’s groups again:

  1. id -nG
sammy sudo backup

Our sudo user will now be able to take advantage of its membership in the backup group.

Next, we need to make the /var/lib/mysql directory and its subdirectories accessible to the mysql group by adding group execute permissions. Otherwise, the backup user will be unable to enter those directories, even though it is a member of the mysql group.

Note: If the value of datadir was not /var/lib/mysql when you checked inside of MySQL earlier, substitute the directory you discovered in the commands that follow.

To give the mysql group access to the MySQL data directories, type:

  1. sudo find /var/lib/mysql -type d -exec chmod 750 {} \;

Our backup user now has the access it needs to the MySQL directory.

Creating the Backup Assets

Now that MySQL and system backup users are available, we can begin to set up the configuration files, encryption keys, and other assets that we need to successfully create and secure our backups.

Create a MySQL Configuration File with the Backup Parameters

Begin by creating a minimal MySQL configuration file that the backup script will use. This will contain the MySQL credentials for the MySQL user.

Open a file at /etc/mysql/backup.cnf in your text editor:

  1. sudo nano /etc/mysql/backup.cnf

Inside, start a [client] section and set the MySQL backup user and password user you defined within MySQL:


Save and close the file when you are finished.

Give ownership of the file to the backup user and then restrict the permissions so that no other users can access the file:

  1. sudo chown backup /etc/mysql/backup.cnf
  2. sudo chmod 600 /etc/mysql/backup.cnf

The backup user will be able to access this file to get the proper credentials but other users will be restricted.

Create a Backup Root Directory

Next, create a directory for the backup content. We will use /backups/mysql as the base directory for our backups:

  1. sudo mkdir -p /backups/mysql

Next, assign ownership of the /backups/mysql directory to the backup user and group ownership to the mysql group:

  1. sudo chown backup:mysql /backups/mysql

The backup user should now be able to write backup data to this location.

Create an Encryption Key to Secure the Backup Files

Because backups contain all of the data from the database system itself, it is important to secure them properly. The xtrabackup utility has the ability to encrypt each file as it is backed up and archived. We just need to provide it with an encryption key.

We can create an encryption key within the backup root directory with the openssl command:

  1. printf '%s' "$(openssl rand -base64 24)" | sudo tee /backups/mysql/encryption_key && echo

It is very important to restrict access to this file as well. Again, assign ownership to the backup user and deny access to all other users:

  1. sudo chown backup:backup /backups/mysql/encryption_key
  2. sudo chmod 600 /backups/mysql/encryption_key

This key will be used during the backup process and any time you need to restore from a backup.

Creating the Backup and Restore Scripts

We now have everything we need to perform secure backups of the running MySQL instance.

In order to make our backup and restore steps repeatable, we will script the entire process. We will create the following scripts:

  • backup-mysql.sh: This script backs up the MySQL databases, encrypting and compressing the files in the process. It creates full and incremental backups and automatically organizes content by day. By default, the script maintains 3 days worth of backups.
  • extract-mysql.sh: This script decompresses and decrypts the backup files to create directories with the backed up content.
  • prepare-mysql.sh: This script “prepares” the back up directories by processing the files and applying logs. Any incremental backups are applied to the full backup. Once the prepare script finishes, the files are ready to be moved back to the data directory.

You can view the scripts in the repository for this tutorial on GitHub at any time. If you do not want to copy and paste the contents below, you can download them directly from GitHub by typing:

  1. cd /tmp
  2. curl -LO https://raw.githubusercontent.com/do-community/ubuntu-1604-mysql-backup/master/backup-mysql.sh
  3. curl -LO https://raw.githubusercontent.com/do-community/ubuntu-1604-mysql-backup/master/extract-mysql.sh
  4. curl -LO https://raw.githubusercontent.com/do-community/ubuntu-1604-mysql-backup/master/prepare-mysql.sh

Be sure to inspect the scripts after downloading to make sure they were retrieved successfully and that you approve of the actions they will perform. If you are satisfied, mark the scripts as executable and then move them into the /usr/local/bin directory by typing:

  1. chmod +x /tmp/{backup,extract,prepare}-mysql.sh
  2. sudo mv /tmp/{backup,extract,prepare}-mysql.sh /usr/local/bin

Next, we will set up each of these scripts and discuss them in more detail.

Create the backup-mysql.sh Script

If you didn’t download the backup-mysql.sh script from GitHub, create a new file in the /usr/local/bin directory called backup-mysql.sh:

  1. sudo nano /usr/local/bin/backup-mysql.sh

Copy and paste the script contents into the file:


export LC_ALL=C

days_of_backups=3  # Must be less than 7
todays_dir="${parent_dir}/$(date +%a)"
now="$(date +%m-%d-%Y_%H-%M-%S)"
processors="$(nproc --all)"

# Use this to echo to standard error
error () {
    printf "%s: %s\n" "$(basename "${BASH_SOURCE}")" "${1}" >&2
    exit 1

trap 'error "An unexpected error occurred."' ERR

sanity_check () {
    # Check user running the script
    if [ "$(id --user --name)" != "$backup_owner" ]; then
        error "Script can only be run as the \"$backup_owner\" user"
    # Check whether the encryption key file is available
    if [ ! -r "${encryption_key_file}" ]; then
        error "Cannot read encryption key at ${encryption_key_file}"

set_options () {
    # List the xtrabackup arguments

    # Add option to read LSN (log sequence number) if a full backup has been
    # taken today.
    if grep -q -s "to_lsn" "${todays_dir}/xtrabackup_checkpoints"; then
        lsn=$(awk '/to_lsn/ {print $3;}' "${todays_dir}/xtrabackup_checkpoints")
        xtrabackup_args+=( "--incremental-lsn=${lsn}" )

rotate_old () {
    # Remove the oldest backup in rotation
    day_dir_to_remove="${parent_dir}/$(date --date="${days_of_backups} days ago" +%a)"

    if [ -d "${day_dir_to_remove}" ]; then
        rm -rf "${day_dir_to_remove}"

take_backup () {
    # Make sure today's backup directory is available and take the actual backup
    mkdir -p "${todays_dir}"
    find "${todays_dir}" -type f -name "*.incomplete" -delete
    xtrabackup "${xtrabackup_args[@]}" --target-dir="${todays_dir}" > "${todays_dir}/${backup_type}-${now}.xbstream.incomplete" 2> "${log_file}"
    mv "${todays_dir}/${backup_type}-${now}.xbstream.incomplete" "${todays_dir}/${backup_type}-${now}.xbstream"

sanity_check && set_options && rotate_old && take_backup

# Check success and print message
if tail -1 "${log_file}" | grep -q "completed OK"; then
    printf "Backup successful!\n"
    printf "Backup created at %s/%s-%s.xbstream\n" "${todays_dir}" "${backup_type}" "${now}"
    error "Backup failure! Check ${log_file} for more information"

The script has the following functionality:

  • Creates an encrypted, compressed full backup the first time it is run each day.
  • Generates encrypted, compressed incremental backups based on the daily full backup when called again on the same day.
  • Maintains backups organized by day. By default, three days of backups are kept. This can be changed by adjusting the days_of_backups parameter within the script.

When the script is run, a daily directory is created where timestamped files representing individual backups will be written. The first timestamped file will be a full backup, prefixed by full-. Subsequent backups for the day will be incremental backups, indicated by an incremental- prefix, representing the changes since the last full or incremental backup.

Backups will generate a file called backup-progress.log in the daily directory with the output from the most recent backup operation. A file called xtrabackup_checkpoints containing the most recent backup metadata will be created there as well. This file is needed to produce future incremental backups, so it is important not to remove it. A file called xtrabackup_info, which contains additional metadata, is also produced but the script does not reference this file.

When you are finished, save and close the file.

Next, if you haven’t already done so, make the script executable by typing:

  1. sudo chmod +x /usr/local/bin/backup-mysql.sh

We now have a single command available that will initiate MySQL backups.

Create the extract-mysql.sh Script

Next, we will create the extract-mysql.sh script. This will be used to extract the MySQL data directory structure from individual backup files.

If you did not download the script from the repository, create and open a file called extract-mysql.sh in the /usr/local/bin directory:

  1. sudo nano /usr/local/bin/extract-mysql.sh

Inside, paste the following script:


export LC_ALL=C

processors="$(nproc --all)"

# Use this to echo to standard error
error () {
    printf "%s: %s\n" "$(basename "${BASH_SOURCE}")" "${1}" >&2
    exit 1

trap 'error "An unexpected error occurred.  Try checking the \"${log_file}\" file for more information."' ERR

sanity_check () {
    # Check user running the script
    if [ "${USER}" != "${backup_owner}" ]; then
        error "Script can only be run as the \"${backup_owner}\" user"
    # Check whether the qpress binary is installed
    if ! command -v qpress >/dev/null 2>&1; then
        error "Could not find the \"qpress\" command.  Please install it and try again."
    # Check whether any arguments were passed
    if [ "${number_of_args}" -lt 1 ]; then
        error "Script requires at least one \".xbstream\" file as an argument."
    # Check whether the encryption key file is available
    if [ ! -r "${encryption_key_file}" ]; then
        error "Cannot read encryption key at ${encryption_key_file}"

do_extraction () {
    for file in "${@}"; do
        base_filename="$(basename "${file%.xbstream}")"
        printf "\n\nExtracting file %s\n\n" "${file}"
        # Extract the directory structure from the backup file
        mkdir --verbose -p "${restore_dir}"
        xbstream -x -C "${restore_dir}" < "${file}"


        xtrabackup "${xtrabackup_args[@]}" --target-dir="${restore_dir}"
        find "${restore_dir}" -name "*.xbcrypt" -exec rm {} \;
        find "${restore_dir}" -name "*.qp" -exec rm {} \;
        printf "\n\nFinished work on %s\n\n" "${file}"
    done > "${log_file}" 2>&1

sanity_check && do_extraction "$@"

ok_count="$(grep -c 'completed OK' "${log_file}")"

# Check the number of reported completions.  For each file, there is an
# informational "completed OK".  If the processing was successful, an
# additional "completed OK" is printed. Together, this means there should be 2
# notices per backup file if the process was successful.
if (( $ok_count !=  $# )); then
    error "It looks like something went wrong. Please check the \"${log_file}\" file for additional information"
    printf "Extraction complete! Backup directories have been extracted to the \"restore\" directory.\n"

Unlike the backup-mysql.sh script, which is designed to be automated, this script is designed to be used intentionally when you plan to restore from a backup. Because of this, the script expects you to pass in the .xbstream files that you wish to extract.

The script creates a restore directory within the current directory and then creates individual directories within for each of the backups passed in as arguments. It will process the provided .xbstream files by extracting directory structure from the archive, decrypting the individual files within, and then decompressing the decrypted files.

After this process has completed, the restore directory should contain directories for each of the provided backups. This allows you to inspect the directories, examine the contents of the backups, and decide which backups you wish to prepare and restore.

Save and close the file when you are finished. Afterward, ensure that the script is executable by typing:

  1. sudo chmod +x /usr/local/bin/extract-mysql.sh

This script will allow us to expand individual backup files into the directory structure needed to restore.

Create the prepare-mysql.sh Script

Finally, download or create the prepare-mysql.sh script within the /usr/local/bin directory. This script will apply the logs to each backup to create a consistent database snapshot. It will apply any incremental backups to the full backup to incorporate the later changes.

Create the script file in your text editor if you did not download it earlier:

  1. sudo nano /usr/local/bin/prepare-mysql.sh

Inside, paste the following contents:


export LC_ALL=C

shopt -s nullglob
incremental_dirs=( ./incremental-*/ )
full_dirs=( ./full-*/ )
shopt -u nullglob


# Use this to echo to standard error
error() {
    printf "%s: %s\n" "$(basename "${BASH_SOURCE}")" "${1}" >&2
    exit 1

trap 'error "An unexpected error occurred.  Try checking the \"${log_file}\" file for more information."' ERR

sanity_check () {
    # Check user running the script
    if [ "${USER}" != "${backup_owner}" ]; then
        error "Script can only be run as the \"${backup_owner}\" user."

    # Check whether a single full backup directory are available
    if (( ${#full_dirs[@]} != 1 )); then
        error "Exactly one full backup directory is required."

do_backup () {
    # Apply the logs to each of the backups
    printf "Initial prep of full backup %s\n" "${full_backup_dir}"
    xtrabackup --prepare --apply-log-only --target-dir="${full_backup_dir}"
    for increment in "${incremental_dirs[@]}"; do
        printf "Applying incremental backup %s to %s\n" "${increment}" "${full_backup_dir}"
        xtrabackup --prepare --apply-log-only --incremental-dir="${increment}" --target-dir="${full_backup_dir}"
    printf "Applying final logs to full backup %s\n" "${full_backup_dir}"
    xtrabackup --prepare --target-dir="${full_backup_dir}"

sanity_check && do_backup > "${log_file}" 2>&1

# Check the number of reported completions.  Each time a backup is processed,
# an informational "completed OK" and a real version is printed.  At the end of
# the process, a final full apply is performed, generating another 2 messages.
ok_count="$(grep -c 'completed OK' "${log_file}")"

if (( ${ok_count} == ${#full_dirs[@]} + ${#incremental_dirs[@]} + 1 )); then
    cat << EOF
Backup looks to be fully prepared.  Please check the "prepare-progress.log" file
to verify before continuing.

If everything looks correct, you can apply the restored files.

First, stop MySQL and move or remove the contents of the MySQL data directory:
        sudo systemctl stop mysql
        sudo mv /var/lib/mysql/ /tmp/
Then, recreate the data directory and  copy the backup files:
        sudo mkdir /var/lib/mysql
        sudo xtrabackup --copy-back --target-dir=${PWD}/$(basename "${full_backup_dir}")
Afterward the files are copied, adjust the permissions and restart the service:
        sudo chown -R mysql:mysql /var/lib/mysql
        sudo find /var/lib/mysql -type d -exec chmod 750 {} \\;
        sudo systemctl start mysql
    error "It looks like something went wrong.  Check the \"${log_file}\" file for more information."

The script looks in the current directory for directories beginning with full- or incremental-. It uses the MySQL logs to apply the committed transactions to the full backup. Afterwards, it applies any incremental backups to the full backup to update the data with the more recent information, again applying the committed transactions.

Once all of the backups have been combined, the uncommitted transactions are rolled back. At this point, the full- backup will represent a consistent set of data that can be moved into MySQL’s data directory.

In order to minimize chance of data loss, the script stops short of copying the files into the data directory. This way, the user can manually verify the backup contents and the log file created during this process, and decide what to do with the current contents of the MySQL data directory. The commands needed to restore the files completely are displayed when the command exits.

Save and close the file when you are finished. If you did not do so earlier, mark the file as executable by typing:

  1. sudo chmod +x /usr/local/bin/prepare-mysql.sh

This script is the final script that we run before moving the backup files into MySQL’s data directory.

Testing the MySQL Backup and Restore Scripts

Now that the backup and restore scripts are on the server, we should test them.

Perform a Full Backup

Begin by calling the backup-mysql.sh script with the backup user:

  1. sudo -u backup backup-mysql.sh
Backup successful! Backup created at /backups/mysql/Thu/full-04-20-2017_14-55-17.xbstream

If everything went as planned, the script will execute correctly, indicate success, and output the location of the new backup file. As the above output indicates, a daily directory (“Thu” in this case) has been created to house the day’s backups. The backup file itself begins with full- to express that this is a full backup.

Let’s move into the daily backup directory and view the contents:

  1. cd /backups/mysql/"$(date +%a)"
  2. ls
backup-progress.log full-04-20-2017_14-55-17.xbstream xtrabackup_checkpoints xtrabackup_info

Here, we see the actual backup file (full-04-20-2017_14-55-17.xbstream in this case), the log of the backup event (backup-progress.log), the xtrabackup_checkpoints file, which includes metadata about the backed up content, and the xtrabackup_info file, which contains additional metadata.

If we tail the backup-progress.log, we can confirm that the backup completed successfully.

  1. tail backup-progress.log
170420 14:55:19 All tables unlocked 170420 14:55:19 [00] Compressing, encrypting and streaming ib_buffer_pool to <STDOUT> 170420 14:55:19 [00] ...done 170420 14:55:19 Backup created in directory '/backups/mysql/Thu/' 170420 14:55:19 [00] Compressing, encrypting and streaming backup-my.cnf 170420 14:55:19 [00] ...done 170420 14:55:19 [00] Compressing, encrypting and streaming xtrabackup_info 170420 14:55:19 [00] ...done xtrabackup: Transaction log of lsn (2549956) to (2549965) was copied. 170420 14:55:19 completed OK!

If we look at the xtrabackup_checkpoints file, we can view information about the backup. While this file provides some information that is useful for administrators, it’s mainly used by subsequent backup jobs so that they know what data has already been processed.

This is a copy of a file that’s included in each archive. Even though this copy is overwritten with each backup to represent the latest information, each original will still be available inside the backup archive.

  1. cat xtrabackup_checkpoints
backup_type = full-backuped from_lsn = 0 to_lsn = 2549956 last_lsn = 2549965 compact = 0 recover_binlog_info = 0

The example above tells us that a full backup was taken and that the backup covers log sequence number (LSN) 0 to log sequence number 2549956. The last_lsn number indicates that some operations occurred during the backup process.

Perform an Incremental Backup

Now that we have a full backup, we can take additional incremental backups. Incremental backups record the changes that have been made since the last backup was performed. The first incremental backup is based on a full backup and subsequent incremental backups are based on the previous incremental backup.

We should add some data to our database before taking another backup so that we can tell which backups have been applied.

Insert another record into the equipment table of our playground database representing 10 yellow swings. You will be prompted for the MySQL administrative password during this process:

  1. mysql -u root -p -e 'INSERT INTO playground.equipment (type, quant, color) VALUES ("swing", 10, "yellow");'

Now that there is more current data than our most recent backup, we can take an incremental backup to capture the changes. The backup-mysql.sh script will take an incremental backup if a full backup for the same day exists:

  1. sudo -u backup backup-mysql.sh
Backup successful! Backup created at /backups/mysql/Thu/incremental-04-20-2017_17-15-03.xbstream

Check the daily backup directory again to find the incremental backup archive:

  1. cd /backups/mysql/"$(date +%a)"
  2. ls
backup-progress.log incremental-04-20-2017_17-15-03.xbstream xtrabackup_info full-04-20-2017_14-55-17.xbstream xtrabackup_checkpoints

The contents of the xtrabackup_checkpoints file now refer to the most recent incremental backup:

  1. cat xtrabackup_checkpoints
backup_type = incremental from_lsn = 2549956 to_lsn = 2550159 last_lsn = 2550168 compact = 0 recover_binlog_info = 0

The backup type is listed as “incremental” and instead of starting from LSN 0 like our full backup, it starts at the LSN where our last backup ended.

Extract the Backups

Next, let’s extract the backup files to create backup directories. Due to space and security considerations, this should normally only be done when you are ready to restore the data.

We can extract the backups by passing the .xbstream backup files to the extract-mysql.sh script. Again, this must be run by the backup user:

  1. sudo -u backup extract-mysql.sh *.xbstream
Extraction complete! Backup directories have been extracted to the "restore" directory.

The above output indicates that the process was completed successfully. If we check the contents of the daily backup directory again, an extract-progress.log file and a restore directory have been created.

If we tail the extraction log, we can confirm that the latest backup was extracted successfully. The other backup success messages are displayed earlier in the file.

  1. tail extract-progress.log
170420 17:23:32 [01] decrypting and decompressing ./performance_schema/socket_instances.frm.qp.xbcrypt 170420 17:23:32 [01] decrypting and decompressing ./performance_schema/events_waits_summary_by_user_by_event_name.frm.qp.xbcrypt 170420 17:23:32 [01] decrypting and decompressing ./performance_schema/status_by_user.frm.qp.xbcrypt 170420 17:23:32 [01] decrypting and decompressing ./performance_schema/replication_group_members.frm.qp.xbcrypt 170420 17:23:32 [01] decrypting and decompressing ./xtrabackup_logfile.qp.xbcrypt 170420 17:23:33 completed OK! Finished work on incremental-04-20-2017_17-15-03.xbstream

If we move into the restore directory, directories corresponding with the backup files we extracted are now available:

  1. cd restore
  2. ls -F
full-04-20-2017_14-55-17/ incremental-04-20-2017_17-15-03/

The backup directories contains the raw backup files, but they are not yet in a state that MySQL can use though. To fix that, we need to prepare the files.

Prepare the Final Backup

Next, we will prepare the backup files. To do so, you must be in the restore directory that contains the full- and any incremental- backups. The script will apply the changes from any incremental- directories onto the full- backup directory. Afterwards, it will apply the logs to create a consistent dataset that MySQL can use.

If for any reason you don’t want to restore some of the changes, now is your last chance to remove those incremental backup directories from the restore directory (the incremental backup files will still be available in the parent directory). Any remaining incremental- directories within the current directory will be applied to the full- backup directory.

When you are ready, call the prepare-mysql.sh script. Again, make sure you are in the restore directory where your individual backup directories are located:

  1. sudo -u backup prepare-mysql.sh
Backup looks to be fully prepared. Please check the "prepare-progress.log" file to verify before continuing. If everything looks correct, you can apply the restored files. First, stop MySQL and move or remove the contents of the MySQL data directory: sudo systemctl stop mysql sudo mv /var/lib/mysql/ /tmp/ Then, recreate the data directory and copy the backup files: sudo mkdir /var/lib/mysql sudo xtrabackup --copy-back --target-dir=/backups/mysql/Thu/restore/full-04-20-2017_14-55-17 Afterward the files are copied, adjust the permissions and restart the service: sudo chown -R mysql:mysql /var/lib/mysql sudo find /var/lib/mysql -type d -exec chmod 750 {} \; sudo systemctl start mysql

The output above indicates that the script thinks that the backup is fully prepared and that the full- backup now represents a fully consistent dataset. As the output states, you should check the prepare-progress.log file to confirm that no errors were reported during the process.

The script stops short of actually copying the files into MySQL’s data directory so that you can verify that everything looks correct.

Restore the Backup Data to the MySQL Data Directory

If you are satisfied that everything is in order after reviewing the logs, you can follow the instructions outlined in the prepare-mysql.sh output.

First, stop the running MySQL process:

  1. sudo systemctl stop mysql

Since the backup data may conflict with the current contents of the MySQL data directory, we should remove or move the /var/lib/mysql directory. If you have space on your filesystem, the best option is to move the current contents to the /tmp directory or elsewhere in case something goes wrong:

  1. sudo mv /var/lib/mysql/ /tmp

Recreate an empty /var/lib/mysql directory. We will need to fix permissions in a moment, so we do not need to worry about that yet:

  1. sudo mkdir /var/lib/mysql

Now, we can copy the full backup to the MySQL data directory using the xtrabackup utility. Substitute the path to your prepared full backup in the command below:

  1. sudo xtrabackup --copy-back --target-dir=/backups/mysql/Thu/restore/full-04-20-2017_14-55-17

A running log of the files being copied will display throughout the process. Once the files are in place, we need to fix the ownership and permissions again so that the MySQL user and group own and can access the restored structure:

  1. sudo chown -R mysql:mysql /var/lib/mysql
  2. sudo find /var/lib/mysql -type d -exec chmod 750 {} \;

Our restored files are now in the MySQL data directory.

Start up MySQL again to complete the process:

  1. sudo systemctl start mysql

Check whether the data has been restored by viewing the contents of the playground.equipment table. Again, you will be prompted for the MySQL root password to continue:

  1. mysql -u root -p -e 'SELECT * FROM playground.equipment;'
+----+-------+-------+--------+ | id | type | quant | color | +----+-------+-------+--------+ | 1 | slide | 2 | blue | | 2 | swing | 10 | yellow | +----+-------+-------+--------+ 2 rows in set (0.02 sec)

Our data has been successfully restored.

After restoring your data, it is important to go back and delete the restore directory. Future incremental backups cannot be applied to the full backup once it has been prepared, so we should remove it. Furthermore, the backup directories should not be left unencrypted on disk for security reasons:

  1. cd ~
  2. sudo rm -rf /backups/mysql/"$(date +%a)"/restore

The next time we need a clean copies of the backup directories, we can extract them again from the backup files.

Creating a Cron Job to Run Backups Hourly

Now that we’ve verified that the backup and restore process are working smoothly, we should set up a cron job to automatically take regular backups.

We will create a small script within the /etc/cron.hourly directory to automatically run our backup script and log the results. The cron process will automatically run this every hour:

  1. sudo nano /etc/cron.hourly/backup-mysql

Inside, we will call the backup script with the systemd-cat utility so that the output will be available in the journal. We’ll mark them with a backup-mysql identifier so we can easily filter the logs:

sudo -u backup systemd-cat --identifier=backup-mysql /usr/local/bin/backup-mysql.sh

Save and close the file when you are finished. Make the script executable by typing:

  1. sudo chmod +x /etc/cron.hourly/backup-mysql

The backup script will now run hourly. The script itself will take care of cleaning up backups older than three days ago.

We can test the cron script by running it manually:

  1. sudo /etc/cron.hourly/backup-mysql

After it completes, check the journal for the log messages by typing:

  1. sudo journalctl -t backup-mysql
-- Logs begin at Wed 2017-04-19 18:59:23 UTC, end at Thu 2017-04-20 18:54:49 UTC. -- Apr 20 18:35:07 myserver backup-mysql[2302]: Backup successful! Apr 20 18:35:07 myserver backup-mysql[2302]: Backup created at /backups/mysql/Thu/incremental-04-20-2017_18-35-05.xbstream

Check back in a few hours to make sure that additional backups are being taken.


In this guide, we’ve installed the Percona Xtrabackup tools to help create live snapshots of our MySQL data on a regular basis. We configured a MySQL and system backup user, set up an encryption key to secure our backup files, and then set up scripts to automate parts of the backup and restore procedures.

The backup script generates a full backup at the start of each day and incremental backups every hour afterwards, keeping three days of backups at any time. The encrypted files and the encryption key can be used in conjunction with other backup technologies to transfer the data off-site for safekeeping. The extract and prepare scripts let us assemble the backups for the day into a consistent set of data that can be used to restore the system.

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Be sure that all files in /var/lib/mysql/ can be accessed by mysql

When making backup, I got InnoDB error 13: mysql has no permission to folder.

I just:

sudo chown -R mysql:mysql /var/lib/mysql

and everything started working.

The presence of high-quality guides like this are one reason that I, as a new developer, am using DigitalOcean.

This is a really good script and guide. However, the backup script has one major flaw: Each time the script will run, it will attempt to do a backup regardless if there’s a running instance of xtrabackup or not… causing misbehavior sometimes on replication databases.

The script simply assumes that the backups and incremental backups will be done in an hour, there are databases where taking a full snapshot and increments can take HOURS…

I recommend adding an additional sanity check at the very beginning of the script to check if xtrabackup is already running and to quit if that is the case:

function CheckProcessStatus {
if pgrep -x $1 > /dev/null
    echo "$1 is Running"
    echo "$1 is not Running"
return "$retval"

function RunPs {
if [ $running_flag -eq 0 ]; then
  echo "no running backup confirmed, moving forward with backup script"
  echo "backup is already running, exiting  with code 1"
  exit 1


CheckProcessStatus "xtrabackup"
echo "flag is $ps_flag"
RunPs $ps_flag

Otherwise, xtrabackup, specially if running on a replication host, it will attempt to stop the replication IO thread, and cause stupid errors in the progress log, and can cause additional issues. One day I ssh’ed on the replication host and the replication had stopped for HOURS for no reason… Even worse… Sometimes the script wouldn’t take a full snapshot because of concurrent running increments…

Everytime i add a new database stop working backup.

All new directories become 700 permission. To fix this read:


How can I change the backup script to take full backup only on Saturdays and incremental in other days?

Just a quick note, in case anyone finds it useful.

I am doing this tutorial on an Ubuntu 18 install (with MySQL 8) and when running the initial full backup, I got this error:

“Access denied; you need (at least one of) the BACKUP_ADMIN privilege(s) for this operation”

After some Googling around I managed to fix this by granting BACKUP_ADMIN rights to the backup user. You can do so by performing the following query in Mysql (as root user):


  • Note that I added BACKUP_ADMIN as a grant for the backup user.

I hope this helps anyone!

Amazingly well written, thank you!

Great article, Thanks!!

Hi, thanks for this.

It works great with xtrabackup version 2.3.10 (based on MySQL server 5.6.24) but I am having trouble getting it working with xtrabackup version 2.0.8 (for Percona Server 5.1.59) against mysql Ver 14.14 Distrib 5.1.73, for redhat-linux-gnu (x86_64) using readline 5.1.

Is there a version of your script that works with the above mysql/xtrabackup versions?

What a great guide! Thank you very much

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