Resolving MySQL binlog.index Missing Error After XtraBackup Restore on CentOS 8

1. Environment

The test was performed on a CentOS 8 (x86) server running MySQL 8.0.18 with Percona XtraBackup 8.0.10 as the backup tool.

Server OS

Database Version

Backup Tool

CentOS 8 for X86

MySQL 8.0.18

XtraBackup 8.0.10

2. Problem

After a successful backup‑restore cycle, MySQL failed to start with errors indicating that the binlog file name was missing:

2021-03-08T16:48:08.510032+08:00 0 [Warning] [MY-010097] [Server] Insecure configuration for --secure-file-priv: Current value does not restrict location of generated files.
2021-03-08T16:48:08.510125+08:00 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.18) starting as process 16556
mysqld: File '/var/lib/mysql/.000003' not found (OS errno 2 - No such file or directory)
2021-03-08T16:48:09.196673+08:00 0 [ERROR] [MY-010958] [Server] Could not open log file.
2021-03-08T16:48:09.196787+08:00 0 [ERROR] [MY-010041] [Server] Can't init tc log
2021-03-08T16:48:09.196961+08:00 0 [ERROR] [MY-010119] [Server] Aborting
2021-03-08T16:48:10.632676+08:00 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.18)  MySQL Community Server - GPL.

The issue turned out to be a corrupted binlog.index file that lost the correct binlog name.

3. Test Procedure

The following steps were carried out to reproduce and diagnose the problem:

Create a MySQL 8.0.18 instance and take a full backup with XtraBackup.

Modify the log_bin setting in the new instance’s my.cnf to use a different binlog name, creating the mismatch.

Prepare the backup:

Copy‑back the data to the data directory:

Start MySQL and observe the same missing binlog error.

4. Analysis

Strace was used during the copy‑back phase to capture the system calls made by XtraBackup. The trace revealed that XtraBackup incorrectly rewrote binlog.index , dropping the original binlog filename and leaving a placeholder such as /var/lib/mysql/.000004 .

Further source‑code inspection (see the linked GitHub pull request) shows that the bug was fixed in newer XtraBackup releases (≥ 8.0.25‑17) by correcting the handling of absolute binlog paths.

5. Conclusions

(1) When MySQL fails to start after a backup restore with an error about a missing binlog file, the binlog.index file is often corrupted; rewriting it with the correct binlog name and restarting resolves the issue.

(2) Users of Percona XtraBackup versions from percona‑xtrabackup‑8.0.6 to percona‑xtrabackup‑8.0.23‑16 should be aware of this bug if the log_bin option contains an absolute path; upgrading to a version that includes the fix (e.g., 8.0.25‑17 ) is recommended.

6. References & Further Reading

Strace usage guide: One Question One Experiment – Table Cache

GDB debugging guide: One Question One Experiment – MySQL Crash Analysis

Compiling XtraBackup from source: Percona Documentation

Bug‑fix commit: GitHub

Linux open() man page: open(2)