Help with Install on RHEL9

[tjkautz]

Hi elabFTW friends,
I am hoping to get some assistance with an install on RHEL9. I will start by saying I am not the best at Linux and using command line.

I am trying to use Podman since that is the 'recommended' method with RHEL9 rather than Docker.

I am running as root for this testing.
I am able to install and start elabftw but when I go to initialize, I get the following MySQL errors:

[root@******]# sudo bash elabctl initialize

      _          _     _____ _______        __
  ___| |    __ _| |__ |  ___|_   _\ \      / /
 / _ \ |   / _| | '_ \| |_    | |  \ \ /\ / / 
|  __/ |__| (_| | |_) |  _|   | |   \ V  V /  
 \___|_____\__,_|_.__/|_|     |_|    \_/\_/   
                                              

Info: using elabctl configuration file: using default values (no config file found)
Info: using elabftw configuration file: /etc/elabftw.yml
---------------------------------------------

In Db.php line 52:
                                                                                            
  SQLSTATE[HY000] [2002] php_network_getaddresses: getaddrinfo for mysql failed: Try again  
                                                                                            

In Db.php line 52:
                                                                                         
  PDO::__construct(): php_network_getaddresses: getaddrinfo for mysql failed: Try again  
                                                                                         

db:install [-r|--reset]

I checked the status of the containers and found the mysql container not working:

CONTAINER ID  IMAGE                            COMMAND     CREATED     STATUS                            PORTS                 NAMES
ae1676471aa4  docker.io/library/mysql:8.0      mysqld      7 days ago  Exited (1) 7 days ago (starting)                        mysql
7812c6182293  docker.io/elabftw/elabimg:5.0.4  /init       7 days ago  Up 7 days                         0.0.0.0:443->443/tcp  elabftw

I restarted the containers and the same error happens on the mysql image.
I have looked at the mysql logs and see the logs filled with this same error:

2024-07-03 18:26:53+02:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 8.0.38-1.el9 started.
find: '/var/lib/mysql/': Permission denied
find: '/var/lib/mysql': Permission denied

Could this be firewall related? We also have SELinux running (per security policy at our institution). I have followed the linux guide but this is what I am getting.

Any help or suggestions would be greatly appreciated.

Thank you,
Tom

[NicolasCARPi]

Hello Tom 👋

Here are a few pointers:

• as a beginner, I'd recommend sticking to the official, documented process, which is docker and docker-compose. Podman works fine, but is not as documented and easy to deploy than docker + a compose file.
• the fact that you think a filesystem permission issue could be firewall related confirms without a doubt that you are a beginner ;) , and that's okay, we all started as beginners, learning by doing mistakes, that's not really an issue. But here you are embarking in an undocumented adventure without any experience administrating GNU/Linux boxes. So my advice is to stick to the documented process (SELinux shouldn't cause issues), and later, if you want, you can explore using Podman, but there isn't really a good reason to do so.
• when you are the root user, no need to use sudo in front of commands
• this page can help: https://doc.elabftw.net/debug.html (but I guess you already figured out how to read logs)

In your particular case, it seems the starting script for MySQL cannot properly start, but you didn't describe how you bind mounted the volume, and where. Is it on a special partition, what are the permissions?

use Podman since that is the 'recommended' method with RHEL9 rather than Docker.

Don't believe the hype. Docker is going strong ;)

[tjkautz]

Hi Nicolas,
Thank you so much for your reply. I am sorry for the delay in response to your note. I've had some vacation and other projects come up.

Yes, I am newb with Linux. My background is supporting Windows environments but am working to expand my knowledge.

For what it's worth, I followed your install guide as closely as I could. Showing my beginner skills, could you further explain what you mean by "describe how you bind mounted the volume, and where."? Could permissions keep the MySQL script from running? (e.g. execute isn't part of the permissions set for some reason?) Assuming yes but wanted to confirm.

Thanks again for your reply and these support forums/tools you have created.

Take care,
Tom

[alexander-haller]

Post your /etc/elabftw.yml - remove secrets, keys and passwords from it.

[NicolasCARPi]

You can do so with: grep -vE "^[[:blank:]]*#|^[[:blank:]]*$" /etc/elabftw.yml | grep -vE "PASSWORD|SECRET_KEY"

Could permissions keep the MySQL script from running?

Yes. Try and change the "volumes:" section of the MySQL container to some other place to see if it helps, here you don't give enough information to help figure things out, that's why we ask for the config file as a start.

[tjkautz]

Hi Alexander-Haller and Nicolas,
Thank you very much for your response. I took your advice, had the server rebuilt and started from scratch with Docker. It was successful and now have it running. I really appreciate you taking the time to provide help and input.
Take care,
-Tom