How to Repair MySQL Database in Linux?

Summary: Read this blog to find out how to repair MySQL database in Linux manually or by using MySQL database repair software. Use the software to recover all the database components without affecting the original database file. You can download the free demo version of the software to preview all the recoverable database components. 

When running the MySQL database on a Linux machine, the database can become corrupt due to several reasons, such as virus attack on the machine, hardware failure, etc. You can try restoring the database from an updated backup. However, if the backup isn’t available, you can try repairing the MySQL database.

Methods to Repair MySQL Database in Linux

Method 1 – Repairing MySQL Database Manually

Note: The manual step-wise approach to repair MySQL database may differ depending on the storage engine you’re using: InnoDB or MyISAM. Thus, troubleshooting database corruption by executing different manual steps requires time, increasing the database downtime. Use a MySQL database repair tool to quickly repair corrupt database and restore it to the original form.   

Here, we will discuss step-wise process to repair a corrupt MySQL database on a Linux-based system:

Step 1: Back up your Database

Make sure to back up your database before attempting to repair it. Doing so will prevent your database from further loss. To back up your MySQL database files, follow these steps:

1 Log in to your server via SSH

2. Stop your MySQL server by using any of the following commands based on your Linux distribution:

For CentOS and Fedora, enter:

service mysqld stop

For Ubuntu and Debian, enter:

service mysql stop

3. To back up your database file, type:

cp -r /var/lib/mysql /var/lib/mysql_backup

4. Restart the MySQL server by running the following command in your Linux system:

service mysqld start

Step 2: Run “mysqlcheck” to Check and Repair MySQL Databases

Note: The mysqlcheck command is useful for users who want to repair MySQL database and tables without stopping MySQL service.

Once you’ve backed up your databases, run the mysqlcheck command to check and repair database and tables for MyISAM or InnoDB database engines. Follow these steps to use mysqlcheck for repairing the database:

1. As the root user, enter the below command:

cd /var/lib/mysql

2. Check the database and all its tables for corruption by typing the command:

mysqlcheck database_name

To check a specific database table for errors, type the command:

mysqlcheck database_name table_name

3. If the table is not corrupted, an OK message is displayed. However, if the database table displays any errors, you need to repair it by using the following command:

mysqlcheck –r database_name table_name

If running the mysqlcheck command does not fix the issue, proceed to the next step.

Step 3: Perform Engine-specific Diagnostics

Run diagnostics specific to the storage engine (InnoDB or MyISAM) used by the database and tables. Follow the appropriate procedure below for your table’s database storage engine.

Repairing MyISAM tables with myisamchk

When your database runs on MyISAM storage engine, run the myisamchk command to repair it. To do this, follow these steps:

Note: The myisamchk command works for the MyISAM storage engine only.

1. Stop your server using any of the below commands for your Linux distribution:

For CentOS and Fedora, use:

service mysqld stop

For Debian and Ubuntu, use:

service mysql stop

2. Type the following:

cd /var/lib/mysql

Change the above directory with the directory where your corrupt database is located. For instance, if the database is named db1, type cd db1.

3. Check corrupt tables in the database, by using the following command:

myisamchk table_name

To check all of the database tables, type the following command:

myisamchk *.MYI

4. Once you have identified the corrupted tables in the database, use the mysqlchk command to repair the tables by following this command:

myisamchk –recover table

5. Restart the server:

For CentOS and Fedora, type:

service mysqld start

For Debian and Ubuntu, type:

service mysql start

Running the InnoDB Recovery Process

To repair db running on InnoDB storage engine, follow these steps:

  1. Open MySQL configuration file “my.cnf”. The location of the my.cnf file will vary depending on your Linux OS. On CentOS and Fedora, you can find the file in the ‘/etc’ directory. And on Debian and Ubuntu, the configuration file is located in the ‘/etc/mysql’ directory.
  2. Once you’ve located my.cnf file, find the [mysqld] section.
  3. In the [mysqld] section, add the following line:

4. Save the changes to the MySQL configuration file, and then restart the MySQL server:

For CentOS and Fedora:

service mysqld restart

For Debian and Ubuntu:

service mysql restart

5. Run the below command to export all of the databases to the databasesbkp.sql file:

mysqldump –all-databases > databasesbkp.sql

6. Start the mysql service, then use the DROP DATABASE command to try to drop the affected database.

Note: If you’re unable to drop a database, delete it manually after stopping the MySQL server.

7. Stop MySQL Server.

8. Type the following command to delete the database manually:

cd /var/lib/mysql rm -rf database

Replace ‘database’ with the name of your database that you want to repair.

9. Open my.cnf file again, and comment out the following line:


This will disable the InnoDB recovery mode.

10. Save the changes you’ve made to my.cnf file, and then start your MySQL Server.

11. Try restoring the database from the backup created in Step 5:

mysql < databasesbkp.sql

Now check the restored database. If the problem persists, use a specialized MySQL database repair software to restore the database.

Method 2 – Repairing MySQL Database with Stellar Repair for MySQL

Stellar Repair for MySQL is a powerful MySQL database repair software recommended by DBAs to repair severely corrupted databases and restore all its objects. The software allows repairing MySQL database on Linux as well as Windows system.

To repair a corrupted MySQL database created on a Linux system, follow these steps:

Step 1: Download and install the software. For software installation, open the Linux Terminal, and then enter the following command:

$ sudo yum install app_name

Note: Here “app_name” is the path of Stellar Repair for MySQL software package that you need to install.

Step 2: Launch the software. The software main interface opens with an Instruction window. Click OK to proceed.

Stellar Repair for MySQL main interface window

Step 3: In Select Data Folder window, select the version of your MySQL installation, then browse and select the data folder containing the corrupt database.

Select MySQL version

Step 4: The list of the databases stored in the selected data folder is displayed. Select all or specific database that you want to repair, and then click Repair.

Select MySQL databases to be repaired

Step 5: Click OK when the ‘Repair Complete’ dialog box appears.

MySQL database repaired

Step 6: The software displays preview of the recoverable MySQL database components.

Preview recoverable MySQL database components

Step 7: Click Save on File menu for saving the repaired MySQL database file.

Step 8: In the ‘Save Database’ dialog box, choose MySQL under Save As, and then enter the required details to connect to your MySQL server. Click Save for saving the repaired database file in MySQL Server.  

MySQL repaired database file saving options

Step 9: A ‘Save Complete’ message box is displayed when the repaired file saving process is complete.

After executing these steps, the MySQL database will be repaired.


Repairing MySQL database in Linux-based system using the manual method does not guarantee to restore all the database components. It might work to fix minor database issues but fail to fix a heavily damaged MySQL database. Using Stellar Repair for MySQL software can help you repair a severely corrupt database and recover all its components, preserving the original file structure and contents.

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