Installatin issue on Ubuntu 20.04 LTS (Focal Fossa)

[Vincent Arsenault]

Hi,

I have followed the installation guide on the site for the 2.8 version of AtoM.

I finished all of the steps, but there is something wrong I can't seems to understand.

Here what I see at the URL :

[��� 8.0.36-0ubuntu0.20.04.1�:��� AGz2+ �ےےے �ےك ����������H "J ]Mzgq _�caching_sha2_password�!�� ے„ #08S01Got packets out of order

What I know : Mysql is running at localhost, Atom and all dependencies are also installed. Composer is installed (globally, is this a issue ?). Php version 7.4 is installed.

Any of you have a idea as where to start my troubleshooting ?

thanks a lot for you help.

Vincent

[Dan Gillean]

Hello Vincent, 

At first glance, at least part of this appears to be a character encoding issue.... however, the error message itself seems to be about MySQL. Let's start by collecting more information. 

• It appears that you are installing AtoM 2.8.0 on an Ubuntu 20.04 server, using PHP 7.4 and MySQL 8 - i.e. you are following the recommended installation docs for the 2.8 version. Is that correct? Is there anything you have changed from the recommended instructions?
• What output do you see if you enter locale into your CLI terminal?
• When creating the database in this step, you definitely used the command as shown there? Were there any problems or errors when creating the database with that character encoding and collation?
• Is this an empty installation, or have you attempted to load data from another source into it? (Alternatively, did you start using it - for example, run a CSV import - and THEN this issue happened?)
• You mentioned composer, which is normally only required if you followed Option 2 in our installation instructions (install from our code repository). Is this what you did, or did you install from the downloadable tarball (Option 1)? Or.... did you run the commands in BOTH sections (Option 1 and 2)?

Now, while we wait for more information from you, I will offer a few initial suggestions to try. 

First, let's double-check that your terminal is properly configured to use UTF-8 by default. If you are using the default terminal client on Ubuntu, you can right-click, select "Preferences," and in the "Compatibility" tab for your profile, check that the Encoding setting is set to UTF-8. 

As to the error itself - now let's try restarting services, including PHP-FPM and MySQL: 

• sudo systemctl restart php7.4-fpm
• sudo systemctl restart mysql

If you have no data, then let's also try dropping and recreating the database:

• mysql -u username -p -e "DROP DATABASE IF EXISTS atom;"
• mysql -u username -p -e "CREATE DATABASE atom CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci;"
  

Replace the username above with the MySQL username you used during the installation process. We can also run the AtoM upgrade task just to be sure that our database schema is correct (though this shouldn't be necessary - just a precaution): 

• php -d memory_limit=-1 symfony tools:upgrade-sql
  

You may need to repeat the restart commands shown above. Additionally, let's clear the application cache and populate the search index: 

• php symfony cc
• php symfony search:populate

Let us know how it goes! If this doesn't resolve the issue, then hopefully with any additional information you can provide we can offer further suggestions on next steps. 

Cheers, 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

he / him

--
You received this message because you are subscribed to the Google Groups "AtoM Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ica-atom-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/bfe37cd0-a0b9-4f26-aaec-5ea3a6bef8e4n%40googlegroups.com.

[Vincent Arsenault]

Hello Dan,

I'm working with Ubuntu 20.04 but the desktop version, could it be an issue ?

I was indeed following the 2.8 doc. and changed nothing from it.

I'll start from scratch today. 

One issue I had was that at some point they ask me for a database password that I'm supposed to have set 'earlier' but can't seem to recall that I have created a password.

I used option 2, when trying with option1 I didn't have the permission to create /usr/share/nginx/atom without the sudo command.

I give another try to the .tar installation in option 1.

Thanks for your help, 

you gave many good routes to look at.

I'll keep you posted

[Vincent Arsenault]

I have redone all of the installation guide, same result for now.

When running the "locale" command, I can tell I'm using utf-8.

When creating the database no error was prompt.

All was done as it is shown in the guide. All except the php symfony tools:install. I had to use sudo because if not, I had the following error:

Failed to make cache directory " ...../atom/cache/qubit/cli/config" while generating cache for configuration file.

When using sudo  php symfony tools:install I was able to install and input all the host, port, user, password and stuff there.

 I also have run the rest of the installation.

Thanks again for your help

Vincent

[Vincent Arsenault]

When I tried to connect with port 3306, I still get the random characters. But without any port, I get a Atom error, so progress have been made, I guess.... 

[Vincent Arsenault]

Here's a error log I was able to retrieve with 

• sudo tail -f /var/log/nginx/error.log

[Dan Gillean]

Hi Vincent, 

I am trying to get some developer time to review this thread and provide some input on possible causes and next steps. It appears that the system isn't finding your files or database tables in the expected locations. 

In the meantime, let's make sure that it's not a filesystem permissions issue, and gather some more information that might help the devs offering advice. 

Normally, AtoM expects all files and directories below the root installation directory (i.e. /usr/share/nginx/atom, per the recommended installation instructions) to be owned by the www-data user. We can ensure these permissions are properly set with: 

• sudo chown -R www-data:www-data /usr/share/nginx/atom
  

It's also possible to declare a specific user when using sudo, so if you ever need to add sudo to a Symfony command to get it to run, you can specify the www-data user explicitly, as in this example below for the search index repopulation command: 

• sudo -u www-data php symfony search:populate

Note that this is specifically for Symfony commands - the www-data user does not own system processes, like services - so when restarting PHP-FPM for example, it's not needed: 

• sudo systemctl restart php7.4-fpm

Note as well that all Symfony commands should be run from AtoM's root installation directory (/usr/share/nginx/atom), otherwise they may not work (you will generally get an error message like "Could not open input file:symfony" or similar).

As to the errors - I am not sure why it is not finding PHP-FPM, or the base objects table in your database. Let's at least make sure that something is there. 

If you change directories to the expected location (/usr/share/nginx/atom) and run the ls command to look around, do you see the expected AtoM files and folders? You should see files and directories similar to what you see in our code repository: 

• https://github.com/artefactual/atom
  

Let's also confirm that the PHP pool was created as expected during installation. Can you access the following file and see a PHP configuration block?

• sudo nano /etc/php/7.4/fpm/pool.d/atom.conf

This configuration file should have been created during installation, and its contents should match this block from the docs: 

• https://www.accesstomemory.org/docs/2.8/admin-manual/installation/ubuntu/#php-fpm
  

Next, let's access the MySQL command-prompt. First, let's double-check the credentials used and the database name given - we can do this by looking at what information got saved and stored in the config/config.php file during installation. From AtoM's root installation directory, run: 

• sudo nano config/config.php

Don't share your credentials here for security purposes, but can you confirm that the database created during installation was in fact named atom?

Now, using the credentials listed in the config file, let's access the MySQL command prompt. See: 

• https://www.accesstomemory.org/docs/latest/admin-manual/maintenance/common-atom-queries/#accessing-the-mysql-command-prompt
  

Once accessed, let's try: 

• DESCRIBE object;

Does this output a table?

Additionally, you could try: 

• SHOW TABLES; 

This should output a list of all the database tables for the selected database (defined when we accessed the MySQL prompt - i.e. atom). You should see several dozen, including object, information_object, information_object_i18n, accession, actor, and many more. If you'd like a whole list, you can see the latest database schema diagram on our wiki here: 

• https://wiki.accesstomemory.org/Development/ERDs#July_2023
  

You can leave the MySQL command prompt by entering exit. 

In any case, hopefully checking on the obvious elements above and ensuring the permissions are correct will help with information gathering, and will allow us to rule out some more obvious potential causes. Let us know what you find, and I will have a developer follow up from there. 

Cheers, 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

he / him

To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/56b8967a-5af3-4817-8cd9-917b45f8d8e2n%40googlegroups.com.

[Vincent Arsenault]

Amazing, thanks for the reply ! 

I'm currently working on it so I'll give all this a try, and let you know how it goes.

This morning I did run a symfony purge, and now I'm able to connect to the url, from the host device with localhost and from other device also with the host ip.

I see all the correct info from my build (site title, description etc)

But, when I input the ip with the port (eg: 192.168.x.x:3306) I still get the random character things. 

When connecting should I input the port number or only the IP ? 

thanks for the support

[Dan Gillean]

Hi Vincent, 

That port is used by the database itself - it should not be needed to access the site in a browser. Try it without! 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

he / him

To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/05ef2406-ead0-4141-8f6e-343a19fbaff5n%40googlegroups.com.