AtoM 2.4 upgrade to 2.6

[Jim McGrath (uOttawa)]

I am in the process of upgrading our DEV environment to 2.6 for testing and have run into an issue with percona-server-server-5.6.  I have followed the instructions to do the upgrade (upgraded Ubunto from 16 to 18) and then did an 'install' of 2.6 as directed.

When I get to the line to install elasticsearch (sudo apt install elasticsearch) it returns with an error that it can't remove percona-server-server-5.6 and I can't go any further, it never does install elasticsearch.  I have searched around but haven't found anything that has worked.  

Did I miss a step somewhere that I am unaware of?

[Ghislain Thibault]

Hi,

I’ll look around tomorrow morning and get back to you as soon as possible. And will ask Dan as well.

Thanks,

Ghislain

 

De : ica-ato...@googlegroups.com <ica-ato...@googlegroups.com> De la part de Jim McGrath (uOttawa)
Envoyé : 22 septembre 2021 16:07
À : AtoM Users <ica-ato...@googlegroups.com>
Objet : [atom-users] AtoM 2.4 upgrade to 2.6

 

Attention : courriel externe | external email

I am in the process of upgrading our DEV environment to 2.6 for testing and have run into an issue with percona-server-server-5.6.  I have followed the instructions to do the upgrade (upgraded Ubunto from 16 to 18) and then did an 'install' of 2.6 as directed.

 

When I get to the line to install elasticsearch (sudo apt install elasticsearch) it returns with an error that it can't remove percona-server-server-5.6 and I can't go any further, it never does install elasticsearch.  I have searched around but haven't found anything that has worked.  

 

Did I miss a step somewhere that I am unaware of?

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[Jim McGrath (uOttawa)]

After going through a dozen webpages and trying every suggested fix to correct the problem, I rolled back to a previous snapshot directly after the OS upgrade (Ubuntu 18.04 with AtoM 2.4).  I followed the instructions again for installing AtoM 2.6 and get through the first 3 commands just fine (download mysql-apt-config, install mysel-apt-config with Legacy Authentication, sudo apt update) but when I do the actual mysql-server install is when it barfs again on trying to remove percona-server-server-5.6.  It spits out a "installed percona-server-server-5.6 package post-removal script subprocess returned error exit status 127" and "subprocess /usr/bin/dpkg returned an error code (1)".  It refuses to go any further, it won't uninstall previous MySQL or install the new MySQL which prevents me from continuing with the install instructions.

[Jim Adamson]

I expect you've already thought of it, but I'd be tempted to provision a new, clean 18.04 server for 2.6, then migrate the data across from the 2.4 server. I don't know if this is an option for you, though.

Thanks, Jim

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Facilities Management Systems
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[Dan Gillean]

Hi Jim (McGrath), 

I agree with Jim (Adamson) - if installing on a fresh server and then migrating your content is an option, I think this will avoid a lot of headaches. 

Barring that, I found an older post with some suggestions for fully removing MySQL/Percona, that might help clear things out so you can install Elasticsearch 5.6 and MySQL 8.0 from scratch for the 2.6 upgrade. Hope this helps:

• https://georgechilumbu.wordpress.com/2016/12/11/uninstall-mysqlpercona-completely/
  

Cheers, 

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

@accesstomemory

he / him

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[Jim McGrath (uOttawa)]

Unfortunately, installing on a fresh server would require completion of a new SID (security documentation detailing server/service/port/firewall requirements, software installed, databases required, on/off campus accessibility, DNS entries, etc) which is a long drawn out process and can take months to be reviewed and approved before the new VM is setup for us to install the OS and AtoM components.  Not a timeline that we are looking at.

The link you provided looks like it finally removed all the components that were stuck.  I will need to review next week and install the AtoM components and do testing.

[Jim McGrath (uOttawa)]

It would seem that along with removing all of the components of the stuck percona-server-server-5.6 install, it also turfed out our SQL database for the site.  Back to square one again.  Am I using the correct "upgrade" instructions to go from 2.4 to 2.6?

[Dan Gillean]

Hi Jim, 

The instructions for an upgrade from any version (after ICA-AtoM 1.1) to 2.6 are here: 

• https://www.accesstomemory.org/docs/2.6/admin-manual/installation/upgrading/
  

Cheers, 

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

@accesstomemory

he / him

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[Jim McGrath (uOttawa)]

OK, that is the one that I am using, and it's not working properly.  I'll restore a snapshot again and do another run through.

[Jim McGrath (uOttawa)]

I restored the DEV system to a stable environment and upgraded Ubuntu to 18.04 and it immediately broke AtoM.  Am I missing a critical step in the upgrade?  I continue the instructions for the install of AtoM 2.6, most of the installs bring back a message that the latest version is already installed.  When I get to the web installer, the web server is running but AtoM comes back with a "500 Internal Server Error" and that I should post a message here LOL

I have followed the instructions and run through the 'upgrade' for AtoM at least a dozen times, and it hasn't been successful once.  Or is the alternative to our server upgrade is to build a complete new server and restore the data?

[Dan Gillean]

Hi Jim, 

I am really sorry to hear that you've had so many issues with this. 

AtoM is unfortunately not really designed to be upgraded in place, so the alternative you describe is currently kind of the correct way - you should create a brand new installation of AtoM separate from the existing one, and then move your data into it. 

One option you might consider would be using virtual machines on your server, so you can create a separate Ubuntu 18.04 installation environment inside a VM without having to disrupt other existing applications on the server. I'm an archivist so my experience in guiding you here is limited, but I know that despite using Linux under the hood, this is how our Support team manages our hosted client instances. 

Alternatively, at this point if there is nothing else on the server, then I'd suggest just wiping it entirely (once you are certain that your data backups are somewhere safe!) so you can properly install and configure Ubuntu 18.04 before proceeding, and then be able to start the AtoM 2.6 installation with a clean environment. 

I'm hoping that other users with similar experiences might be able to chime in with some suggestions that will help you move forward with the least amount of pain!

Cheers, 

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

@accesstomemory

he / him

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[Jim McGrath (uOttawa)]

The server I am working on is a DEV environment on a physical box.  I would never attempt to test a system upgrade on a production system.  Of which, the production server is a VM.  Creating a new separate production VM would involve security documentation (as I previously posted) and it could take weeks to months to be processed to a state where we could actually perform the install of AtoM.

Even if we do bring up a completely new server/install of AtoM 2.6, it needs to be tested in DEV/QA, to document the procedure so that when we proceed to production, we have the least amount of downtime as possible.

[Monica Wood]

Hi Jim,

I just want to make sure you are installing the new version of atom into a new directory and not trying to overwrite the version that is already there.

Before you upgrade, make sure you have a copy of your database (as the database server will be removed and reinstalled) and data files, then move the old version of atom aside into another completely different directory.

After you have upgraded from 16.04 -> 18.04:

It sounds like your server is using percona mysql server, instead of the default mysql server. So you will need to stop the mysql service and either upgrade that package to the equivalent percona server for mysql8 version, or uninstall percona before installing the mysql8 packages as described in the documentation.

Hopefully the rest of the install instructions will work as normal.  

* Double check the elasticsearch version that is already installed, as you may not need to reinstall this.

* Make sure your nginx configuration is pointing to the place you will install the new version of atom.

* PHP version is updated, so you will need to check the correct php modules are installed and things are set up correctly using php 7.2

Install Atom as per the instructions: https://www.accesstomemory.org/en/docs/2.6/admin-manual/installation/linux/ubuntu-bionic/#download-atom 

including creating the database and running the web installer.

You will want a blank/fresh copy of atom 2.6 running. as pointed to here: https://www.accesstomemory.org/en/docs/2.6/admin-manual/installation/upgrading/#install-the-latest-version-of-atom

Once this is installed and you can log in, follow the rest of the instructions on the upgrading document.

* copy your data files from the old atom (uploads/downloads dir)

* Drop the new database, recreate it (to remove the files the new install put into it)

* Load the DB dump you took before upgrading to Ubuntu 18.04 into the newly created database

All the above commands are available: https://www.accesstomemory.org/en/docs/2.6/admin-manual/installation/upgrading/#copy-your-old-data 

Lastly run the upgrade task to migrate the data, reindex etc and restart the services.

Let us know how you go.

Cheers,

Monica Wood

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[Jim McGrath (uOttawa)]

I reviewed the 'upgrade' document, and I can see that there is no mention that the new AtoM 2.6 was to be in a different directory.  Nor does it say to backup the database beforehand.  It does say AFTER the new AtoM is installed to copy the old data, but I have never been able to get to that point.  I did create a new database when I configured SQL.

As for percona, was it not the default for AtoM 2.4?  I followed those instructions and got our current DEV/PROD environments up and running properly.

I'll restore a snapshot again and proceed with the modified instructions you indicated and see if that resolves the problems.  Thank you for the info!