Docker - Atom 2.6 MYSQL Percona permissions problem

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José Anjos

Jul 15, 2020, 10:00:23 AM7/15/20
to AtoM Users
I'm trying to setup Atom 2.6 with Docker.
All the containers start except percona:8.0 docker_percona_1
Doing docker logs --follow I have this:

mysqld: File './binlog.index' not found (OS errno 13 - Permission denied)
2020-07-15T11:46:18.340436Z 0 [Warning] [MY-010915] [Server] 'NO_ZERO_DATE', 'NO_ZERO_IN_DATE' and 'ERROR_FOR_DIVISION_BY_ZERO' sql modes should be used with strict mode. They will be merged with strict mode in a future release.
2020-07-15T11:46:18.340592Z 0 [Warning] [MY-010091] [Server] Can't create test file /var/lib/mysql/mysqld_tmp_file_case_insensitive_test.lower-test
2020-07-15T11:46:18.340738Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.19-10) starting as process 1
2020-07-15T11:46:18.345608Z 0 [Warning] [MY-010091] [Server] Can't create test file /var/lib/mysql/mysqld_tmp_file_case_insensitive_test.lower-test
2020-07-15T11:46:18.345627Z 0 [Warning] [MY-010159] [Server] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive
2020-07-15T11:46:18.346461Z 0 [ERROR] [MY-010119] [Server] Aborting
2020-07-15T11:46:18.346654Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.19-10)  Percona Server (GPL), Release 10, Revision f446c04.
mysqld: File './binlog.index' not found (OS errno 13 - Permission denied)
2020-07-15T12:05:59.705886Z 0 [Warning] [MY-010915] [Server] 'NO_ZERO_DATE', 'NO_ZERO_IN_DATE' and 'ERROR_FOR_DIVISION_BY_ZERO' sql modes should be used with strict mode. They will be merged with strict mode in a future release.

José Raddaoui

Jul 15, 2020, 10:47:52 AM7/15/20
to AtoM Users
Hi José,

Are you recreating the environment over a previous version setup? You may need to remove the volume that was used by the previous Percona version. If you want to maintain your database you'll need to crate a dump from it and store it outside the container. Then run "down --volumes" and "up -d" again, then restore the dump and populate the search index if needed. Please, let me know if that helps or if you need more information.

Best regards,

José Anjos

Jul 16, 2020, 5:08:51 AM7/16/20
to AtoM Users
Yes that is the problem.
I thought I could use multiple versions in separated folders (Ex: Atom254, Atom26, etc)
and they start isolated.
I've deleted everything and now it's ok.
Thank you very much José

David TG

Sep 24, 2022, 12:59:12 PM9/24/22
to AtoM Users
I have the same issue and I want to retrieve the DB before deleting. Is that possible? 

Dan Gillean

Sep 26, 2022, 8:40:48 AM9/26/22
to ICA-AtoM Users
Hi David, 

I don't personally use Docker, but yes, I believe it's possible to extract a database dump to your host machine before doing anything else. First you'll access the percona command prompt, then run a sqldump command, and finally copy that dump from the temporary location inside Docker to a location accessible on your host machine. Something like the following: 
  1. docker-compose exec percona bash
  2. mysqldump --no-tablespaces -hlocalhost -uatom -patom_12345 atom > /tmp/dump.sql
  3. [exit the percona command prompt]
  4. cp docker_percona_1:/tmp/dump.sql ./dump.sql
A quick overview of this example, since some elements may be different for your local environment. Make changes as needed:  
  1. Here we enter the percona command prompt
  2. we export a sqldump  called dump.sql to the /tmp directory of the Docker image, using atom as the database user, atom_12345 as the database password, and atom as the database name
  3. We type exit to exit the percona command prompt
  4. We copy the sqldump from our tmp location inside the Docker image to the ./ root directory of our host machine
Let me know if that works - if not, I'll ask one of our developers to follow up. 


Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
he / him

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