If your MySQL server is filling up disk space even though its primary storage is not located on this disk, it’s essential to identify what’s causing this issue. Here’s a detailed exploration of possible causes and solutions:

Possible Causes and Solutions

1. Log Files Accumulation

• Reason: MySQL generates various log files such as binary logs, error logs, slow query logs, and general logs. These logs are often stored on the local disk and can grow rapidly if not managed properly.
• Solution:
  • Review Log Configuration: Check your MySQL configuration (usually in my.cnf or my.ini) for log file paths and sizes. Adjust the log file retention policies and sizes as needed.
  • Enable Log Rotation: Use log rotation tools like logrotate on Linux to manage and compress old log files.
  • Purge Binary Logs: Regularly clean up old binary logs using the PURGE BINARY LOGS command or configure automatic purging by setting expire_logs_days.

   PURGE BINARY LOGS BEFORE 'YYYY-MM-DD HH:MM:SS';

2. Temporary Files and Tables

• Reason: MySQL uses temporary files for operations like sorting, temporary tables, and intermediate query results. These temporary files are typically stored in the /tmp directory or a directory specified by the tmpdir variable.
• Solution:
  • Change Temporary Directory: If possible, set the tmpdir variable in your MySQL configuration to point to a disk with more space.
  [mysqld] tmpdir = /path/to/larger/disk/tmp
  • Monitor and Cleanup: Regularly monitor the tmpdir directory and clean up any orphaned temporary files.

3. InnoDB Storage Location

• Reason: Although you mentioned that the primary storage is not on this disk, InnoDB can create its own temporary files or double-write buffer files on the local disk.
• Solution:
  • Check InnoDB File Paths: Ensure that the innodb_data_home_dir and innodb_log_group_home_dir parameters in your MySQL configuration are pointing to the correct storage location.
  [mysqld] innodb_data_home_dir = /path/to/storage innodb_log_group_home_dir = /path/to/storage

4. Misconfigured File Paths

• Reason: Sometimes, MySQL might be configured to store certain files (like log files, temporary files, or even some data files) on the local disk by default.
• Solution:
  • Review and Correct Paths: Verify all file path settings in the MySQL configuration to ensure they are correctly pointing to the desired storage location.

5. Backup and Snapshot Files

• Reason: If backups or snapshots are stored on the local disk, they can quickly consume large amounts of space.
• Solution:
  • Relocate Backups: Configure your backup software to store backups on a separate disk or remote storage.
  • Automate Cleanup: Implement automated scripts to move or delete old backup files.

6. Misleading Disk Usage Reports

• Reason: Tools like du and df might show high disk usage due to files that are deleted but still held open by MySQL processes.
• Solution:
  • Restart MySQL: Restarting the MySQL server can release these file handles, effectively freeing up space.Use lsof: Use the lsof command to identify open files that are consuming space.
  lsof | grep deleted

7. Swap Usage

• Reason: If your system is using swap heavily, it could be an indication of insufficient memory, causing MySQL to write more temporary files to disk.
• Solution:
  • Increase Memory: Ensure your server has sufficient RAM for the MySQL workload.
  • Optimize Queries: Reduce memory usage by optimizing queries and adjusting MySQL memory settings.

8. MySQL Plugin or Third-Party Tools

• Reason: Some plugins or third-party tools may create their own files or logs on the local disk.
• Solution:
  • Review Plugins: Check for any installed plugins or tools that might be generating files.
  • Consult Documentation: Refer to the documentation for these plugins or tools to understand their storage requirements.

Diagnostic Steps

1. Check Disk Usage:

• Use commands like du -sh /path/to/disk/* and df -h to identify which directories or files are consuming the most space.

   du -sh /var/lib/mysql/*
   df -h

2. Identify MySQL File Locations:

• Look at MySQL’s configuration file (my.cnf or my.ini) to identify where it stores different types of files.

   cat /etc/my.cnf

3. Monitor MySQL Processes:

• Use SHOW PROCESSLIST and SHOW VARIABLES to get insights into what MySQL is currently doing and its configuration.

   SHOW PROCESSLIST;
   SHOW VARIABLES LIKE 'tmpdir';

4. Inspect Log Files:

• Check MySQL’s log files for any messages indicating high disk usage or other issues.

   tail -f /var/log/mysql/error.log

Preventative Measures

• Regular Maintenance: Schedule regular maintenance tasks like log rotation, temporary file cleanup, and database optimization.
• Monitoring and Alerts: Set up monitoring tools and alerts to notify you when disk usage is approaching critical levels.
• Configuration Management: Regularly review and update MySQL configuration to ensure it aligns with your storage and performance needs.
• Capacity Planning: Plan and provision enough storage capacity based on your current and projected workload to avoid running out of space.

By systematically diagnosing and addressing these potential issues, you can prevent MySQL from filling up your disk space and ensure it operates smoothly.