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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

2020-03-09T05:14:56.631119Z 0 [System] [MY-010910] [Server] /opt/bitnami/mysql/bin/mysqld.bin: Shutdown complete (mysqld 8.0.15) MySQL Community Server - GPL.
2020-03-09T05:16:56.071411Z 0 [System] [MY-010116] [Server] /opt/bitnami/mysql/bin/mysqld.bin (mysqld 8.0.15) starting as process 4893
2020-03-09T05:16:56.074734Z 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.
2020-03-09T05:16:56.074743Z 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.
2020-03-09T05:16:56.083922Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_actionscheduler_groups.ibd'
2020-03-09T05:16:56.083944Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_db_scheduler.ibd'
2020-03-09T05:16:56.083964Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_ac_abandoned_cart_history_lite.ibd'
2020-03-09T05:16:56.083984Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_auto_updates.ibd'
2020-03-09T05:16:56.084009Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_wp_scheduler.ibd'
2020-03-09T05:16:56.084032Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_tm_taskmeta.ibd'
2020-03-09T05:16:56.084053Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_wc_tax_rate_classes.ibd'
2020-03-09T05:16:56.084075Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_update_log.ibd'
2020-03-09T05:16:56.084097Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_actionscheduler_logs.ibd'
2020-03-09T05:16:56.084119Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_oses_emails.ibd'
2020-03-09T05:16:56.084151Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_login_log.ibd'
2020-03-09T05:16:56.084172Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_oses_clicks.ibd'
2020-03-09T05:16:56.084191Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_wfls_2fa_secrets.ibd'
2020-03-09T05:16:56.084212Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_ac_guest_abandoned_cart_history_lite.ibd'
2020-03-09T05:16:56.084234Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_ac_sent_history_lite.ibd'
2020-03-09T05:16:56.084255Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_wfls_settings.ibd'
2020-03-09T05:16:56.084275Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_block_single_ip.ibd'
2020-03-09T05:16:56.084296Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_plugin_settings.ibd'
2020-03-09T05:16:56.084317Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_block_range_ip.ibd'
2020-03-09T05:16:56.084338Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_wc_product_meta_lookup.ibd'
2020-03-09T05:16:56.084358Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_sbi_instagram_posts.ibd'
2020-03-09T05:16:56.084379Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_sbi_instagram_feeds_posts.ibd'
2020-03-09T05:16:56.084402Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_cleanup_optimizer_licensing.ibd'
2020-03-09T05:16:56.084423Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_ac_email_templates_lite.ibd'
2020-03-09T05:16:56.084442Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_actionscheduler_claims.ibd'
2020-03-09T05:16:56.084463Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_tm_tasks.ibd'
2020-03-09T05:16:56.084485Z 1 [Warning] [MY-012197] [InnoDB] Unable to open './bitnami_wordpress/wp_actionscheduler_actions.ibd'
2020-03-09T05:16:56.112313Z 1 [ERROR] [MY-012961] [InnoDB] Only one log file found
2020-03-09T05:16:56.112332Z 1 [ERROR] [MY-012930] [InnoDB] Plugin initialization aborted with error not found.
2020-03-09T05:16:56.713336Z 1 [ERROR] [MY-010334] [Server] Failed to initialize DD Storage Engine
2020-03-09T05:16:56.713530Z 0 [ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
2020-03-09T05:16:56.713868Z 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.

Improve this question
2
  • You might have to perform a restore. Do you have a backup of the database?
    – John K. N.
    Mar 9, 2020 at 12:19
  • Sadly this is an old client's website, they reached out cause of this error so i dont have access to one :(
    – Nickey K
    Mar 9, 2020 at 12:29

1 Answer 1

Reset to default
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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

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1
  • 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"
    – Nickey K
    Mar 9, 2020 at 12:36

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