[bitnami/mysql] [ERROR] [MY-010020] [Server] Data Dictionary initialization failed.

[RishiDixit1]

Name and Version

bitnami/mysql:8.0.37-debian-12-r2

What architecture are you using?

amd64

What steps will reproduce the bug?

while deploying bitnami mysql helm charts , pods are going into CrashLoopBackOff state.

chart version : mysql-11.1.14 APP VERSION: 8.4.2

What is the expected behavior?

pods must be running fine.

What do you see instead?

pods are going into CrashLoopBackOff state, , here are the error logs of the pods.

mysql 12:58:48.50 INFO  ==> 
mysql 12:58:48.51 INFO  ==> ** Starting MySQL setup **
mysql 12:58:48.53 INFO  ==> Validating settings in MYSQL_*/MARIADB_* env vars
mysql 12:58:48.53 INFO  ==> Initializing mysql database
mysql 12:58:48.54 WARN  ==> The mysql configuration file '/opt/bitnami/mysql/conf/my.cnf' is not writable. Configurations based on environment variables will not be applied for this file.
mysql 12:58:48.54 INFO  ==> Installing database
2024-08-01T12:58:48.565692Z 0 [System] [MY-013169] [Server] /opt/bitnami/mysql/bin/mysqld (mysqld 8.0.39) initializing of server in progress as process 36
2024-08-01T12:58:48.567224Z 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.
2024-08-01T12:58:48.575873Z 0 [Warning] [MY-010001] [Server] Can't create thread to handle bootstrap (errno: 1)
2024-08-01T12:58:48.575919Z 0 [ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
2024-08-01T12:58:48.575931Z 0 [ERROR] [MY-013236] [Server] The designated data directory /bitnami/mysql/data/ is unusable. You can remove all files that the server added to it.
2024-08-01T12:58:48.575939Z 0 [ERROR] [MY-010119] [Server] Aborting
2024-08-01T12:58:48.576347Z 0 [System] [MY-010910] [Server] /opt/bitnami/mysql/bin/mysqld: Shutdown complete (mysqld 8.0.39)  Source distribution.

Additional information

mysql 12:58:48.50 INFO  ==> 
mysql 12:58:48.51 INFO  ==> ** Starting MySQL setup **
mysql 12:58:48.53 INFO  ==> Validating settings in MYSQL_*/MARIADB_* env vars
mysql 12:58:48.53 INFO  ==> Initializing mysql database
mysql 12:58:48.54 WARN  ==> The mysql configuration file '/opt/bitnami/mysql/conf/my.cnf' is not writable. Configurations based on environment variables will not be applied for this file.
mysql 12:58:48.54 INFO  ==> Installing database
2024-08-01T12:58:48.565692Z 0 [System] [MY-013169] [Server] /opt/bitnami/mysql/bin/mysqld (mysqld 8.0.39) initializing of server in progress as process 36
2024-08-01T12:58:48.567224Z 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.
2024-08-01T12:58:48.575873Z 0 [Warning] [MY-010001] [Server] Can't create thread to handle bootstrap (errno: 1)
2024-08-01T12:58:48.575919Z 0 [ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
2024-08-01T12:58:48.575931Z 0 [ERROR] [MY-013236] [Server] The designated data directory /bitnami/mysql/data/ is unusable. You can remove all files that the server added to it.
2024-08-01T12:58:48.575939Z 0 [ERROR] [MY-010119] [Server] Aborting
2024-08-01T12:58:48.576347Z 0 [System] [MY-010910] [Server] /opt/bitnami/mysql/bin/mysqld: Shutdown complete (mysqld 8.0.39)  Source distribution.

[RishiDixit1]

@javsalgar can you please support on this please, i have tried with latest helm chart with all latest bitnami/mysql images.

[javsalgar]

Hi,

Are you performing an upgrade of an existing mysql installation? Which is the PVC technology you are using? Maybe it is incompatible

[RishiDixit1]

@javsalgar , I am doing a fresh installation in Robin cluster, with robin storage class. for PVC technology Robin Cloud Native Storage (CNS) is used, attaching the links for your refr. https://docs.robin.io/storage/5.4.8/install.html#

[javsalgar]

Hi,

Thanks for sharing the information. I did not know about this PVC technology. As you are doing a fresh installation, could you try installing with the *.persistence.enabled values to false? Just to ensure the issue is with the PVC technology

[RishiDixit1]

hi @javsalgar after doing persistence enable as false pods are going into crashed state as pvc is not created. PVC technology is NFS in the current cluster.

[javsalgar]

Could you elaborate on the exact crash error when persistence is not enabled? What do the logs show? Same error?

[RishiDixit1]

@javsalgar yes same errors and pods are getting into crashed state.

mysql 06:15:33.09 INFO  ==> ** Starting MySQL setup **
mysql 06:15:33.13 INFO  ==> Validating settings in MYSQL_*/MARIADB_* env vars
mysql 06:15:33.13 INFO  ==> Initializing mysql database
mysql 06:15:33.16 WARN  ==> The mysql configuration file '/opt/bitnami/mysql/conf/my.cnf' is not writable. Configurations based on environment variables will not be applied for this file.
mysql 06:15:33.16 INFO  ==> Installing database
2024-08-13T06:15:33.209087Z 0 [Warning] [MY-010918] [Server] 'default_authentication_plugin' is deprecated and will be removed in a future release. Please use authentication_policy instead.
2024-08-13T06:15:33.209126Z 0 [System] [MY-013169] [Server] /opt/bitnami/mysql/bin/mysqld (mysqld 8.0.39) initializing of server in progress as process 35
2024-08-13T06:15:33.211867Z 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.
2024-08-13T06:15:33.217421Z 0 [Warning] [MY-010001] [Server] Can't create thread to handle bootstrap (errno: 1)
2024-08-13T06:15:33.217464Z 0 [ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
2024-08-13T06:15:33.217473Z 0 [ERROR] [MY-013236] [Server] The designated data directory /bitnami/mysql/data/ is unusable. You can remove all files that the server added to it.
2024-08-13T06:15:33.217480Z 0 [ERROR] [MY-010119] [Server] Aborting
2024-08-13T06:15:33.217914Z 0 [System] [MY-010910] [Server] /opt/bitnami/mysql/bin/mysqld: Shutdown complete (mysqld 8.0.39)  Source distribution.

[javsalgar]

Could you show the pod yaml to ensure that it is using an emptyDir volume? This error is very strange and we cannot reproduce it

[github-actions[bot]]

This Issue has been automatically marked as "stale" because it has not had recent activity (for 15 days). It will be closed if no further activity occurs. Thanks for the feedback.

[github-actions[bot]]

Due to the lack of activity in the last 5 days since it was marked as "stale", we proceed to close this Issue. Do not hesitate to reopen it later if necessary.