Recommended order of upgrades?

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James Elder

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Jun 7, 2021, 11:40:55 AM6/7/21
to AtoM Users
Hi

I am running AtoM on a Virtual Private Server and hadn't dared do any upgrades until I had figured out how to improve my backup arrangements. Having now worked out how to mount Dropbox as a drive on the VPS, I've been able to backup both data and uploads, which is a great relief.

I'm currently running AtoM 2.4 on Ubuntu 16.04. So, I really ought to upgrade Linux, AtoM, and its components to their current versions.

Any views on 1) the best order to do this and 2) do I need to go from AtoM 2.4 to 2.5 and then to 2.6 or will it be better to go directly from 2.4 to 2.6?

I did actually try upgrading Ubuntu from 16.04 to 18.04 last night and found that this knocked my AtoM site offline, so reverted to an earlier snapshot of the VPS as it was too late on a Sunday evening to start unpicking what the issue was.

If anyone can point me to documentation or threads on possible issues/things to look out for when upgrading Ubuntu, that would be very helpful.

Thankyou!

James

Dan Gillean

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Jun 9, 2021, 9:32:07 AM6/9/21
to ICA-AtoM Users
Hi James, 

I will consult with our team and see if they have any further suggestions, but in general:

You'll definitely want to upgrade the O/S before actually upgrading AtoM, otherwise you might find a mismatch in expected dependency versions or changes in underlying systems that will affect the installation process for AtoM. Ideally, you'd create a separate VM so you can leave the old one in place and make sure you don't have dependency conflicts (such as PHP versions, etc) - but if that's not possible then you may need to deal with some down time for the original site, and should plan on upgrading outside of your normal business hours or known points of high traffic. 

With the dependencies, make sure you look at the Requirements and Installation doc pages closely, in case some parameters have changed - you can miss this if you just try upgrading a dependency like MySQL in place. For example, the collation format has changed in MySQL 8 vs 5.6, but more importantly, in 5.7 and later there are some SQL modes that are enabled by default that don't work with AtoM, so the 2.6 documentation includes a step to create custom SQL modes that was not present in the 2.4 installation documentation. 

In terms of upgrading AtoM, you do not need to upgrade to 2.5 first - you can go straight from 2.4 to 2.6. Once again, be sure to follow the Upgrading documentation closely - in particular, I've noticed that people regularly miss the step where you drop and recreate the database, and this often leads to issues when trying to run the upgrade task! 

Finally, if you have a custom theme, you might want to review the final section in the Upgrading page - we've tried to include some tips of things to consider or changes that might impact a custom theme, requiring a bit more manual intervention during an upgrade. See: 
Hope this helps! 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory
he / him


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James Elder

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Jun 10, 2021, 3:12:08 PM6/10/21
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Thanks Dan!

James Elder

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Jan 4, 2022, 2:36:13 PMJan 4
to AtoM Users
Happy New Year all.

Following on from this discussion last summer, yesterday I had another go at upgrading from Ubuntu 16 to 18 on the VPS which hosts my Atom instance.

All appeared to go smoothly with no apparent error messages but, after the upgrade had completed and I had restarted NGINX, the URL (and the server) which should be providing the AtoM homepage just returned a blank page - no error messages, just blank.

I'm sure I'm probably missing something basic in terms of restarting something or other following an operating system upgrade. Any ideas?

For the time being I've just reverted to a previous snapshot to get the site back online.

One thing I did notice during the upgrade was the message 'Some third party entries in your sources.list were disabled. You can re-enable them after the upgrade with the 'software-properties' tool or your package manager.'

Could that be the cause? I had a look in sources.list after I'd revert to backup and as far as I could see the only entry that this might apply to was elasticsearch, but I don't imagine that would cause AtoM not to display at all?

Thanks for any suggestions

James

Dan Gillean

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Jan 4, 2022, 4:43:28 PMJan 4
to ICA-AtoM Users
Hi James, 

I've not seen that error before, but I did manage to find this thread, which has an explanation and possible solution for that problem: 
You could make a backup of your sources list before retrying the upgrade, and then reapplying it afterwards. I've also found a gist with the default Ubuntu 18.04 sources list here: 
Regarding AtoM not working: 

I will follow up with our team for further suggestions since I'm not a system administrator, but I'll try to offer a few initial thoughts. 

Elasticsearch is necessary for providing search and browse page results, so it definitely could be related. Try re-enabling that source and restarting Elasticsearch to see if it helps. 

If not, then my first suggestion would be to check the Nginx webserver (particularly the config file created during installation at /etc/nginx/sites-available/atom), try reloading it (sudo systemctl reload nginx), and also check for any error messages in the logs: 
Of course, AtoM 2.4 was never tested on Ubuntu 18.04, and there are a number of other differences in the underlying dependencies - for example: 
  • 2.4 uses PHP 7.0 when running Ubuntu 16.04; 2.6 expects PHP 7.2
  • 2.4 used a manually installed php-apcu_bc-beta package because php-apcu was not available in Ubuntu 16.04 at the time. 2.6 can just use php-apcu. 
  • 2.4 uses Elasticsearch 1.7, while 2.6 uses v5.6
  • 2.4 uses MySQL 5.6, while 2.6 uses v8.0
  • etc...
It may be that there is some underlying conflict with the Ubuntu version and the 2.4 dependencies, and that you might just need to do the Ubuntu upgrade at a time when you can immediately work on a new AtoM installation and accept some downtime for your site as you transition - or ideally, set it up in a new VM and then just update the DNS record to point to the new virtual server once you have AtoM 2.6 running. 

I did manage to talk to one AtoM developer still working this afternoon, who basically agreed with this last point. 

I would fall back to our recommended upgrade procedure, i.e. set up a new Ubuntu 18.04 VPS, install AtoM 2.6 according to the installation instructions, migrate and upgrade your database data, and copy over the digital objects, etc. Checking the error logs will hopefully expose the immediate error that is breaking the site, but I expect it may be a rabbit warren of dependency issues and incompatible software versions. Unfortunately, in-place upgrade is generally not the shortcut it looks to be.

So.... with those warnings in mind, start with the suggestions here, and let us know how it goes. If you find anything useful in the webserver error logs but are unsure how to proceed, feel free to share it here, and we'll try to offer further suggestions if we're able. Good luck!

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory
he / him

James Elder

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Jan 4, 2022, 6:02:19 PMJan 4
to AtoM Users
Thanks Dan. As it happens, my VPS provider wants to migrate me to new equipment - although they want me to do that in an automates way that will just create an image of the existing VPS, I will ask if there’s a way I could do it to have both up for a day to give me a chance to do a managed migration and upgrade of both the OS and AtoM.

I’ll have a think about my options.

I am wondering though, could the error I’ve experienced simply be a case that I meed to restart PHP after the Ubuntu upgrade has completed?

James

Dan Gillean

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Jan 5, 2022, 9:12:39 AMJan 5
to ICA-AtoM Users
I am wondering though, could the error I’ve experienced simply be a case that I need to restart PHP after the Ubuntu upgrade has completed?

I don't personally know for sure, but it's worth trying! Hope you find a way forward, James - Good luck!

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory
he / him

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