Various installation issues Atom 2.6

[Matthew Bruton]

I completed installation of atom 2.6 but encountered a number of problems along the way, which I would like to share, as some may find it useful.

I am installing with all the necessary physical requirements for the system and on ubuntu 18.

I followed the installation instructions to the letter. Nonetheless I encountered the following issues:

1. I had to remove the default Php pool in order for the web installer to even come on screen. I tried restarting all services including php before that, but removing the pool seemed to be the only thing which did it.

2. I stalled at when going onto the second config page (insertsql), getting a 502 bad gateway. I got round it by skipping directly to the next page as suggested in earlier threads.

I'm gonna try installing now on a second system and see if I get the same problems. Will update here.

The system I was using had very little to conflict. I was just using sambashare.

[Dan Gillean]

Hi Matthew, 

Thank you for sharing this. We did make a number of memory improvements in AtoM that we were hoping would resolve the web installer issues, but it sounds like people are still seeing them. We hope to remove the web installer component entirely in future releases - all the rest of the installation process takes place on the command-line, and there's no real reason to switch to the web installer for those last steps, especially given that it's causing errors and timeouts. 

That's strange about the web installer not even appearing at all unless you removed the PHP pool. I hope this is not too common an issue (I'll be keeping an eye on reports about this!), and once again, this is something that removing the web installer should hopefully address. 

In the meantime, for anyone who encounters timeout issues using the web installer, this thread has 2 possible workarounds listed. 

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

@accesstomemory

he / him

On Thu, Aug 6, 2020 at 10:52 AM Matthew Bruton <matthewb...@gmail.com> wrote:

I completed installation of atom 2.6 but encountered a number of problems along the way, which I would like to share, as some may find it useful.

I am installing with all the necessary physical requirements for the system and on ubuntu 18.

I followed the installation instructions to the letter. Nonetheless I encountered the following issues:

1. I had to remove the default Php pool in order for the web installer to even come on screen. I tried restarting all services including php before that, but removing the pool seemed to be the only thing which did it.

2. I stalled at when going onto the second config page (insertsql), getting a 502 bad gateway. I got round it by skipping directly to the next page as suggested in earlier threads.

I'm gonna try installing now on a second system and see if I get the same problems.

The system I was using had very little to conflict. I was just using sambashare.

--
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/aca9ef80-3682-48c8-82f8-1517fddc5477o%40googlegroups.com.

[Matthew Bruton]

Thanks Dan,

So I tested it out on a second server, and I am still having problems even getting onto the installation screen.

Both before and after having deleted the default pool.

Restarted pretty much all the services. Restarted whole server. No change.

I am attaching the nginx log and also the atom-worker log, which gives a bit more info. It is something wrong with php alright. Do you recognise these errors? 

I literally have no idea what to do as I can't move beyond this step.

[José Raddaoui]

Hi Matthew,

From those errors, it looks like you're missing PHP's Ctype extension. Is this second server an installation following the docs in Ubuntu 18.04? This extension is usually enabled by default:

https://www.php.net/manual/en/ctype.setup.php

About the web installer timeout, please check this thread instead of the older one for 2.5.x, as the process has changed a bit in AtoM 2.6.

Best regards.

[Matthew Bruton]

Hi Jose,

I am following the installation to the letter. :)

I tried to manually install ctype. The screenshot attached shows what happened.

I am now trying to install a third time on yet another computer starting completely from scratch by installing Ubuntu as a fresh installation. The the second computer is still running, so if you have other suggestions, I am all ears.

Will let you know if it happens in either case.

Incidentally, and probably a second issue, when installing mysql on the first screen I get (see second attachment) I just went for the "ok" option on the bottom. There was nothing in the installation instructions about this particular screen, but I assume this is because I should just click ok. Let me know if I am wrong.

[José Raddaoui]

Hi again Matthew,

Quite rare the Ctype issue, I've never seen it before. There is another error right before the ctype_digit() one in the worker log, that seems to be looking for pdo_mysql.so in a "php/2017..." folder, so maybe there is a mix of PHP versions in that system.

About the first MySQL screen, you picked the right choice. Actually, there is a note about it in the documentation too, but it's not in bold ...

When asked about which product do you wish to configure, leave the defaults, select “Ok” and continue.

I hope everything goes okay this time.

Bests.

[Matthew Bruton]

Update on the third installation.

I got onto the main web installer screen.

It stalled again when I tried to move on.

Changed the fastcgi timeout value, but that didn't work.

Instead I changed the xms heap size as mentioned in previous explanations. That did work.

Artefactual is right to think about changing it to command line only. If someone can manage the previous command line installation of prerequisites, then they can manage the final stage.

[José Raddaoui]

Hi Matthew,

Thanks for reporting what did the trick for you!

Please, could you explain a bit more what have you done? It looks like Elasticsearch 5.x sets the JVM head size to 2 GB, which has been reduced to 1 GB in version 7.x. Did you lower that value? What's the total memory of the server?

Thanks again!

[Matthew Bruton]

I set it to 512 MB. /etc/elasticsearch/jvm.options file that is.

Not sure what the system memory is, but it is over the requirements of Atom.


[matthewb...@gmail.com]

Hi Jose,

I'm getting the same error again here on a totally fresh system.

Any ideas?

[matthewb...@gmail.com]

Update:

I thought that since was a php issue, that I could just purge it and re install. This option did not work.

[José Raddaoui]

Hi Matthew,

Do you mean the Ctype error or the memory issue? Is this instance still using Ubuntu 18.04 and PHP 7.2?

If the issue is a PHP component or dependency missing, purging and reinstalling AtoM won't solve it.

Best regards,

Radda.

[matthewb...@gmail.com]

Radda,

I mean the Ctype error. It is now the second time (maybe third) this has happened. Both systems are completely independent. The second was a fresh install. And both are using the latest installation of atom following all the instructions to the letter.

Would appreciate whatever help you can offer, because this is becoming a challenge. :)

[José Raddaoui]

Hi Matthew,

Indeed, quite a puzzling challenge. I just tested the PHP installation in a new droplet to see if something has changed in Ubuntu 18.04 or their PHP repositories since the last time I did an installation. The steps I followed ...

• Create new droplet (in Digital Ocean 4 GB / 2 CPUs) using the Ubuntu 18.04 (LTS) x64 image.
• Connect through SSH and upgrade the system.
  

            # apt update && apt upgrade

• Check Ubuntu version:

            # lsb_release -a

            No LSB modules are available.

            Distributor ID: Ubuntu

            Description: Ubuntu 18.04.5 LTS

            Release:         18.04

            Codename:         bionic

• Install PHP as in the documentation (see installation command and output).
• Check phpinfo() from the CLI interactive shell (look for ctype in this output).
  • Additional .ini files parsed: /etc/php/7.2/cli/conf.d/20-ctype.ini
    
  • ctype functions => enabled
    
• Verify Ctype works as expected:

            # php -a

            Interactive mode enabled

            php > echo var_dump(ctype_digit('test'));

            bool(false)

            php > echo var_dump(ctype_digit('123'));

            bool(true)

You may find more information checking the phpinfo() output and PHP ini files from your system. This would be for the worker and CLI tasks, if you also have the same issue from the browser, you'll have to check the PHP ini files from the /etc/php/7.2/fpm folder.

Best regards,

Radda.