MySQL Data abnormally growing for unknown reason

Keywords: WordPress - AWS - Technical issue - Other
bnsupport ID: 2ebf2fa1-e0ab-de87-e5e2-92187dde70ac
Description:
Hello,

I’m using a EC2/Linux/Wordpress Stack from Bitnami. About every two weeks my website crashes. I SSH in and see that there is no space left. So I expand my EBS volume in AWS (by 10GB), and restart the instance. The website comes back up again, but then the issue repeats every two weeks or so. My /opt/bitnami/mysql/data size is increasing at around 5GB per week, and I am only adding maybe several KB of data in that time. The symptoms are similar to what was seen in Something Taking Up Space And Growing.

My bin logs were already set to expire every seven days, but I changed that to 1 day. It did not solve the problem. So far I have expanded my server memory from 10GB to 20, then 30, 40, and now 50GB.

Please help me figure out what is growing abnormally.

Hi @editor1,

Thanks for using Bitnami. It seems that MySQL is creating big binlog files in a short period of time. The binlog files contain information about data modifications made by the MySQL server. If the application is performing many changes there, those actions will be recoded in the binlog files.

You can disable the binary logging by checking the information in this other community post

This other thread has useful information about how to disable it and how to purge the information

Happy to help!


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So I added the code to disable bin logs. However, I ran ``bitnami@ip-172-31-73-98:~$ sudo du -hs /opt/bitnami///* | sort -rh | head -35`

I got the following. Can you tell me if the first folder bitnami_wordpress is a bin log that can be deleted? Or is that my wordpress database. It looks like the next two folders contain binlogs.

34G     /opt/bitnami/mysql/data/bitnami_wordpress
1.1G    /opt/bitnami/mysql/data/binlog.000054
900M    /opt/bitnami/mysql/data/binlog.000053
268M    /opt/bitnami/apps/wordpress/htdocs
234M    /opt/bitnami/mysql/data/binlog.000055
130M    /opt/bitnami/mysql/lib/mecab
76M     /opt/bitnami/mysql/data/ibdata1
71M     /opt/bitnami/apache2/var/cache
52M     /opt/bitnami/mysql/bin/mysqld.bin
48M     /opt/bitnami/mysql/data/ib_logfile1
48M     /opt/bitnami/mysql/data/ib_logfile0
42M     /opt/bitnami/apps/phpmyadmin/htdocs
27M     /opt/bitnami/common/lib/libicudata.so.64.2
24M     /opt/bitnami/mysql/data/mysql.ibd
22M     /opt/bitnami/mysql/data/undo_002
22M     /opt/bitnami/mysql/data/undo_001
17M     /opt/bitnami/apache2/modules/libphp7.so
16M     /opt/bitnami/php/bin/php.bin
15M     /opt/bitnami/php/bin/php-cgi.bin
14M     /opt/bitnami/mysql/lib/plugin
12M     /opt/bitnami/php/lib/php
12M     /opt/bitnami/mysql/data/ibtmp1
12M     /opt/bitnami/apache2/logs/access_log
11M     /opt/bitnami/common/share/terminfo
10M     /opt/bitnami/apache2/modules/mod_pagespeed.so
10M     /opt/bitnami/apache2/modules/mod_pagespeed_ap24.so
8.2M    /opt/bitnami/apps/wordpress/bnconfig.disabled
7.2M    /opt/bitnami/mysql/lib/libmysqlrouter.so.1
6.7M    /opt/bitnami/mysql/bin/mysqlpump.bin
6.6M    /opt/bitnami/mysql/lib/libmysqlclient.so.21.0.16
6.6M    /opt/bitnami/mysql/bin/mysqlbinlog
6.6M    /opt/bitnami/mysql/bin/mysql.bin
6.5M    /opt/bitnami/mysql/bin/myisamchk.bin
6.4M    /opt/bitnami/mysql/bin/mysql_upgrade.bin
6.4M    /opt/bitnami/mysql/bin/mysqlslap.bin

34G     /opt/bitnami/mysql/data/bitnami_wordpress
1.1G    /opt/bitnami/mysql/data/binlog.000054
900M    /opt/bitnami/mysql/data/binlog.000053
268M    /opt/bitnami/apps/wordpress/htdocs
234M    /opt/bitnami/mysql/data/binlog.000055
130M    /opt/bitnami/mysql/lib/mecab
76M     /opt/bitnami/mysql/data/ibdata1
71M     /opt/bitnami/apache2/var/cache
52M     /opt/bitnami/mysql/bin/mysqld.bin
48M     /opt/bitnami/mysql/data/ib_logfile1
48M     /opt/bitnami/mysql/data/ib_logfile0
42M     /opt/bitnami/apps/phpmyadmin/htdocs
27M     /opt/bitnami/common/lib/libicudata.so.64.2
24M     /opt/bitnami/mysql/data/mysql.ibd
22M     /opt/bitnami/mysql/data/undo_002
22M     /opt/bitnami/mysql/data/undo_001
17M     /opt/bitnami/apache2/modules/libphp7.so
16M     /opt/bitnami/php/bin/php.bin
15M     /opt/bitnami/php/bin/php-cgi.bin
14M     /opt/bitnami/mysql/lib/plugin
12M     /opt/bitnami/php/lib/php
12M     /opt/bitnami/mysql/data/ibtmp1
12M     /opt/bitnami/apache2/logs/access_log
11M     /opt/bitnami/common/share/terminfo
10M     /opt/bitnami/apache2/modules/mod_pagespeed.so
10M     /opt/bitnami/apache2/modules/mod_pagespeed_ap24.so
8.2M    /opt/bitnami/apps/wordpress/bnconfig.disabled
7.2M    /opt/bitnami/mysql/lib/libmysqlrouter.so.1
6.7M    /opt/bitnami/mysql/bin/mysqlpump.bin
6.6M    /opt/bitnami/mysql/lib/libmysqlclient.so.21.0.16
6.6M    /opt/bitnami/mysql/bin/mysqlbinlog
6.6M    /opt/bitnami/mysql/bin/mysql.bin
6.5M    /opt/bitnami/mysql/bin/myisamchk.bin
6.4M    /opt/bitnami/mysql/bin/mysql_upgrade.bin
6.4M    /opt/bitnami/mysql/bin/mysqlslap.bin

Now I have another problem. I was trying to access phpMyAdmin, and couldn’t. So I used the command to restart all services. MySql would not start! Please help. Here is the output of /opt/bitnami/mysql/data/mysqld.log:

2019-10-31T18:26:38.427285Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427290Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427300Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427310Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427314Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427318Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427323Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427340Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427349Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427354Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427358Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427363Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427370Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427379Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427383Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427388Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427392Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427399Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427408Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427413Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427417Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427421Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427428Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427438Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427442Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427446Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427450Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427460Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427470Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427474Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427478Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427483Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427490Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427499Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427503Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427508Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427512Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427519Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427528Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427533Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427537Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427541Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427548Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427558Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427562Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427566Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427570Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427578Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427587Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427591Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427595Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427600Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427607Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427622Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427627Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427631Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427635Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427643Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427652Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427656Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427660Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427665Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427672Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427681Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427685Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427689Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427694Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427701Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427710Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427714Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427718Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427723Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427730Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427739Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427743Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427748Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427752Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427759Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427771Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427776Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427780Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427784Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427791Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427801Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427805Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427809Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427813Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427821Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427830Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427834Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427838Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427843Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427850Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427859Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427863Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427868Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427872Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427879Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427888Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427892Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427897Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427901Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427908Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427921Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427925Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427929Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427934Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427941Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427950Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427954Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427958Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427963Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427970Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.427979Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.427983Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.427988Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.427992Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.427999Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.428009Z 1935 [ERROR] [MY-012592] [InnoDB] Operating system error number 13 in a file operation.
2019-10-31T18:26:38.428013Z 1935 [ERROR] [MY-012595] [InnoDB] The error means mysqld does not have the access rights to the directory.
2019-10-31T18:26:38.428017Z 1935 [Warning] [MY-012093] [InnoDB] Cannot open './bitnami_wordpress/wp_relevanssi_stopwords.ibd'. Have you deleted .ibd files under a running mysqld server?
2019-10-31T18:26:38.428022Z 1935 [ERROR] [MY-012157] [InnoDB] Trying to do I/O to a tablespace which exists without an .ibd data file. I/O type: read, page: [page id: space=101, page number=4], I/O length: 16384 bytes
2019-10-31T18:26:38.428029Z 1935 [ERROR] [MY-011966] [InnoDB] trying to read page [page id: space=101, page number=4] in nonexisting or being-dropped tablespace
2019-10-31T18:26:38.437237Z 1935 [ERROR] [MY-011825] [InnoDB] [FATAL] Unable to read page [page id: space=101, page number=4] into the buffer pool after 100 attempts. The most probable cause of this error may be that the table has been corrupted. Or, the table was compressed with with an algorithm that is not supported by this instance. If it is not a decompress failure, you can try to fix this problem by using innodb_force_recovery. Please see http://dev.mysql.com/doc/refman/8.0/en/ for more details. Aborting...
2019-10-31T18:26:38.437264Z 1935 [ERROR] [MY-013183] [InnoDB] Assertion failure: ut0ut.cc:629 thread 140674138629888
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/8.0/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
18:26:38 UTC - mysqld got signal 6 ;
Most likely, you have hit a bug, but this error can also be caused by malfunctioning hardware.
Thread pointer: 0x463ccb0
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 7ff1400fdd80 thread_stack 0x46000
/opt/bitnami/mysql/bin/mysqld.bin(my_print_stacktrace(unsigned char*, unsigned long)+0x2e) [0x1d563fe]
/opt/bitnami/mysql/bin/mysqld.bin(handle_fatal_signal+0x323) [0xee86f3]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x11390) [0x7ff154a84390]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x38) [0x7ff152d43428]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x16a) [0x7ff152d4502a]
/opt/bitnami/mysql/bin/mysqld.bin(ut_dbg_assertion_failed(char const*, char const*, unsigned long)+0x2b6) [0x1fdf586]
/opt/bitnami/mysql/bin/mysqld.bin(ib::fatal::~fatal()+0x11a) [0x1fe0b3a]
/opt/bitnami/mysql/bin/mysqld.bin(Buf_fetch<Buf_fetch_normal>::read_page()+0x158) [0x203aed8]
/opt/bitnami/mysql/bin/mysqld.bin(Buf_fetch_normal::get(buf_block_t*&)+0x18) [0x203af98]
/opt/bitnami/mysql/bin/mysqld.bin(Buf_fetch<Buf_fetch_normal>::single_page()+0x33) [0x203ef43]
/opt/bitnami/mysql/bin/mysqld.bin(buf_page_get_gen(page_id_t const&, page_size_t const&, unsigned long, buf_block_t*, Page_fetch, char const*, unsigned long, mtr_t*, bool)+0x19a) [0x2041d9a]
/opt/bitnami/mysql/bin/mysqld.bin(btr_cur_open_at_index_side_func(bool, dict_index_t*, unsigned long, btr_cur_t*, unsigned long, char const*, unsigned long, mtr_t*)+0x37d) [0x201a09d]
/opt/bitnami/mysql/bin/mysqld.bin(row_search_mvcc(unsigned char*, page_cur_mode_t, row_prebuilt_t*, unsigned long, unsigned long)+0x1cb1) [0x1f6a371]
/opt/bitnami/mysql/bin/mysqld.bin(ha_innobase::index_read(unsigned char*, unsigned char const*, unsigned int, ha_rkey_function)+0x29e) [0x1e27d2e]
/opt/bitnami/mysql/bin/mysqld.bin(ha_innobase::index_first(unsigned char*)+0x30) [0x1e0dac0]
/opt/bitnami/mysql/bin/mysqld.bin(handler::ha_index_first(unsigned char*)+0x1f0) [0xfe28e0]
/opt/bitnami/mysql/bin/mysqld.bin(IndexScanIterator<false>::Read()+0x23) [0xd2bca3]
/opt/bitnami/mysql/bin/mysqld.bin(JOIN::exec()+0x493) [0xd91ae3]
/opt/bitnami/mysql/bin/mysqld.bin(Sql_cmd_dml::execute_inner(THD*)+0x2bc) [0xe0eb1c]
/opt/bitnami/mysql/bin/mysqld.bin(Sql_cmd_dml::execute(THD*)+0x3e8) [0xe16878]
/opt/bitnami/mysql/bin/mysqld.bin(mysql_execute_command(THD*, bool)+0x144e) [0xdc5d3e]
/opt/bitnami/mysql/bin/mysqld.bin(mysql_parse(THD*, Parser_state*)+0x31f) [0xdca03f]
/opt/bitnami/mysql/bin/mysqld.bin(dispatch_command(THD*, COM_DATA const*, enum_server_command)+0x2c63) [0xdcd173]
/opt/bitnami/mysql/bin/mysqld.bin(do_command(THD*)+0x18c) [0xdcdc2c]
/opt/bitnami/mysql/bin/mysqld.bin() [0xedab60]
/opt/bitnami/mysql/bin/mysqld.bin() [0x21daf41]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x76ba) [0x7ff154a7a6ba]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d) [0x7ff152e1541d]

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (5afb0a8): SELECT stopword FROM wp_relevanssi_stopwords
Connection ID (thread ID): 1935
Status: NOT_KILLED

The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.

Hi,

We have a Support Tool that will gather relevant information for us to analyze your configuration and logs. Could you please download and execute it on the machine where the stack is running by following the steps described in the guide below?

How to Run the Bitnami Support Tool

Please note that you need to paste the code ID that is shown at the end.

I had to restore my Wordpress site on a different server, which overcame the MySQL crashing issue. The restored instance was 6.6GB a week ago, and it is 12.9GB now. Whatever is growing my database before is doing it again.

My Bitnami Support Tool code is: 2dd0c578-577a-1ea7-73cb-6efa40553f93

Hi @editor1,
Could you take a look to this thread it seems to be a similar issue.
Most probably you have a plugin that is generating a lot of rows in the database.

I looked at the thread… it didn’t really tell me anything. I believe it is a plugin that is causing the issue, and several others are having a similar issue, but there was no clue about which plugin is causing the issue. I ran WP Optimize and it crashed my site, which I had to recover again.

My plan going forward is to run an experiment. I made a clone of my EC2 instance. I deactivated a number of plugins on the cloned instance and after only one day I can see a difference. Immediately after the clone, both instances were at 5.8GB. After 24 hours, the primary instance was up to 6.3GB, and the clone remained at 5.8GB. Next I plan to reactivate, deactivate, etc. until I find the culprit. I will share if I discover a solution.

Hi @editor1,
Maybe if you dig into the data in the tables, similarly as what was done in that thread, you can get which is the culprit in a easier way.
I hope you can find it without to much hassle.

Thanks forehand

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