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Table of Contents
Check disk usage
Clean up binary logs (Binary Logs)
Delete databases or tables that are no longer used
Optimize tablespace and defragmentation
Monitoring and preventive measures
Home Database Mysql Tutorial Troubleshooting MySQL Disk Space Issues and Cleanup

Troubleshooting MySQL Disk Space Issues and Cleanup

Jul 31, 2025 am 03:13 AM
mysql disk space

When the MySQL database has insufficient disk space, you can follow the following steps to check and clean it: 1. Use df -h and du -sh /var/lib/mysql/* to check the disk and MySQL file usage; 2. Clean the binary logs, delete the old logs by time or file name through PURGE BINARY LOGS, or set expire_logs_days to automatically clean up in my.cnf; 3. Delete databases or tables that are no longer used, confirm that they are useless and make backups before executing DROP DATABASE or DROP TABLE; 4. Use OPTIMIZE TABLE to recycle InnoDB tablespace fragments, be careful to reserve enough space to execute; 5. Deploy monitoring tools such as Prometheus and Zabbix Set disk usage alarms and execute cleanup scripts regularly to prevent problems.

Troubleshooting MySQL Disk Space Issues and Cleanup

Insufficient disk space is a common problem during the MySQL database operation, especially when the data volume grows rapidly or log files are not cleaned in time. If this problem is not processed in time, it may cause the database to fail to write new data, service crashes or even downtime. Here are some troubleshooting and cleaning methods to help you quickly deal with insufficient MySQL disk space.

Troubleshooting MySQL Disk Space Issues and Cleanup

Check disk usage

First, you need to confirm whether MySQL really takes up disk space. You can use the following command to view the overall disk usage:

 df -h

If you find that the partition where /var/lib/mysql is located is close to full load, you can basically be sure that MySQL takes up a lot of space.

Troubleshooting MySQL Disk Space Issues and Cleanup

Then enter the MySQL data directory to view the specific file usage:

 du -sh /var/lib/mysql/*

Focus on the size of files such as .ibd files (InnoDB tablespace), ibdata1 (shared tablespace), and mysql-bin.* (binary log).

Troubleshooting MySQL Disk Space Issues and Cleanup

Clean up binary logs (Binary Logs)

If you enable binary logging, they may take up a lot of disk space. By default, these logs are not automatically deleted.

You can check the current binary logs through the following command:

 SHOW BINARY LOGS;

There are two ways to clean up:

  • Clean up by time : For example, keep logs for the last 7 days

     PURGE BINARY LOGS BEFORE NOW() - INTERVAL 7 DAY;
  • Clean by file name : for example, keep all logs before a specific log file

     PURGE BINARY LOGS TO 'mysql-bin.010';

?? Note: If you use master-slave replication, make sure that the slave has read the log to be deleted before performing the cleanup operation.

You can also set an automatic cleaning policy in my.cnf :

 expire_logs_days = 7

Delete databases or tables that are no longer used

Sometimes after the business changes, some old databases or tables are no longer used. You can clean up by following the steps below:

  1. Log in to MySQL and list all databases:

     SHOW DATABASES;
  2. Check whether there are test libraries, temporary libraries, or abandoned business libraries.

  3. If you confirm that you can delete it, execute:

     DROP DATABASE database_name;

For large tables, deletion may affect performance. It is recommended to operate during low peak periods and make backups in advance.


Optimize tablespace and defragmentation

The InnoDB storage engine will produce fragmentation after frequent updates and deletion operations, causing table space to swell. You can use OPTIMIZE TABLE command to recycle space:

 OPTIMIZE TABLE table_name;

This operation will rebuild the table and organize the fragmentation, and is suitable for large tables with frequent data changes.

?? Note: The optimization process requires additional space, so it is necessary to ensure that the disk has enough remaining space to be successfully executed.

If you are using a separate tablespace ( innodb_file_per_table=ON ), the .ibd file of each table will be regenerated; if it is a shared tablespace, the size of ibdata1 will not be reduced.


Monitoring and preventive measures

In addition to temporary cleaning, it is more important to establish a monitoring mechanism to prevent similar problems from happening again:

  • Use monitoring tools such as Prometheus Grafana, Zabbix or cloud platforms to regularly check disk usage trends.
  • Perform table optimization and log cleaning scripts regularly.
  • Set alarm rules to notify the operation and maintenance personnel when the disk usage rate reaches a certain threshold (such as 85%).

Basically these commonly used methods. Although disk space issues seem simple, there are still many details that need to be paid attention to when handling them, especially when operating in production environments.

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