Permissions issues with MYSQL on a Bitnami/Nginx/PHP/WordPress server

Question

i just did restarted services on my Bitnami/Nginx/SSL/WordPress server (was updating my certs).

I suddenly got a disk space full, i found that my issue was Binlogs clogging up, which i promptly deleted and was good to turn it back on. However, now i have a permissions issue.

The MYSQL logs show

2020年03月09日T05:14:56.631119Z 0 [System] [MY-010910] [Server] /opt/bitnami/mysql/bin/mysqld.bin: Shutdown complete (mysqld 8.0.15) MySQL Community Server - GPL.
2020年03月09日T05:16:56.071411Z 0 [System] [MY-010116] [Server] /opt/bitnami/mysql/bin/mysqld.bin (mysqld 8.0.15) starting as process 4893
2020年03月09日T05:16:56.074734Z 0 [Warning] [MY-013242] [Server] --character-set-server: 'utf8' is currently an alias for the character set UTF8MB3, but will be an alias for UTF8MB4 in a future release. Please consider using UTF8MB4 in order to be unambiguous.
2020年03月09日T05:16:56.074743Z 0 [Warning] [MY-013244] [Server] --collation-server: 'utf8_general_ci' is a collation of the deprecated character set UTF8MB3. Please consider using UTF8MB4 with an appropriate collation instead.
2020年03月09日T05:16:56.083922Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_actionscheduler_groups.ibd'
2020年03月09日T05:16:56.083944Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_db_scheduler.ibd'
2020年03月09日T05:16:56.083964Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_ac_abandoned_cart_history_lite.ibd'
2020年03月09日T05:16:56.083984Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_auto_updates.ibd'
2020年03月09日T05:16:56.084009Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_wp_scheduler.ibd'
2020年03月09日T05:16:56.084032Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_tm_taskmeta.ibd'
2020年03月09日T05:16:56.084053Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_wc_tax_rate_classes.ibd'
2020年03月09日T05:16:56.084075Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_update_log.ibd'
2020年03月09日T05:16:56.084097Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_actionscheduler_logs.ibd'
2020年03月09日T05:16:56.084119Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_oses_emails.ibd'
2020年03月09日T05:16:56.084151Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_login_log.ibd'
2020年03月09日T05:16:56.084172Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_oses_clicks.ibd'
2020年03月09日T05:16:56.084191Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_wfls_2fa_secrets.ibd'
2020年03月09日T05:16:56.084212Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_ac_guest_abandoned_cart_history_lite.ibd'
2020年03月09日T05:16:56.084234Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_ac_sent_history_lite.ibd'
2020年03月09日T05:16:56.084255Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_wfls_settings.ibd'
2020年03月09日T05:16:56.084275Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_block_single_ip.ibd'
2020年03月09日T05:16:56.084296Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_plugin_settings.ibd'
2020年03月09日T05:16:56.084317Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_block_range_ip.ibd'
2020年03月09日T05:16:56.084338Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_wc_product_meta_lookup.ibd'
2020年03月09日T05:16:56.084358Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_sbi_instagram_posts.ibd'
2020年03月09日T05:16:56.084379Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_sbi_instagram_feeds_posts.ibd'
2020年03月09日T05:16:56.084402Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_licensing.ibd'
2020年03月09日T05:16:56.084423Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_ac_email_templates_lite.ibd'
2020年03月09日T05:16:56.084442Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_actionscheduler_claims.ibd'
2020年03月09日T05:16:56.084463Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_tm_tasks.ibd'
2020年03月09日T05:16:56.084485Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_actionscheduler_actions.ibd'
2020年03月09日T05:16:56.112313Z 1 [ERROR] [MY-012961] [InnoDB] Only one log file found
2020年03月09日T05:16:56.112332Z 1 [ERROR] [MY-012930] [InnoDB] Plugin initialization aborted with error not found.
2020年03月09日T05:16:56.713336Z 1 [ERROR] [MY-010334] [Server] Failed to initialize DD Storage Engine
2020年03月09日T05:16:56.713530Z 0 [ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
2020年03月09日T05:16:56.713868Z 0 [ERROR] [MY-010119] [Server] Aborting

Anyone know how i can fix permissions? I tried to CHOWN the mysql directory with no luck, i haven't ever seen the ./bitnami_wordpress issue and cannot seem to find a fix online at all.

• John K. N.: You might have to perform a restore. Do you have a backup of the database?
• Nickey K: Sadly this is an old client's website, they reached out cause of this error so i dont have access to one :(

Answer 1

My guess here is you have to check the binary log index first, e.g. locate the binlog.index (in my case this file was in the same directory as binary log files themselfs) and check it's content (the binlog filenames it points to).

To prevent the binlog files using your whole free space, optimize their expire period accordingly in my.ini (cnf), e.g.: binlog_expire_logs_seconds = 259200

• Nickey K: Thanks! I've added the expire logs for future use. I found the binlog.index file in /opt/bitnami/mysql/data folder The permissions on this file are -rw-r----- 1 mysql root 64 Feb 27 02:21 binlog.index Could that be the cause of the "unable to open" message i keep getting? what is the permissions this file should be at? Ps. my user is "bitnami"