Skip to first unread message
Stephen Harding
Mar 31, 2020, 9:19:27 AM3/31/20
to AtoM Users
Hi there,
Firsty I'm a newbie to AtoM and happy to be part of this vibrant community. I'm a developer at Newcastle University and we chose AtoM as our software solution for our Library's Special Collections and Archives department after speaking to many other UK institutions who also use AtoM as well as those who use other solutions.
Server Environment
I've been following the installation instructions for the latest version, 2.5. I'm running a slightly different server environment to that listed within here (Centos 7.7 and using Apache 2.4.6) however I have done the equivelant bits of config including installing all of the various dependencies and extensions required. The server spec exceeds the minimum hardware requirements. All services, e.g. MySQL 8.0.19 are locally hosted on the same server.
Installation - early issues with SELinux
When navigating to the web-based installation I initially hit a few issues due to SELinux, specifically due to filesystem permissions which I was able to fix. Furthermore, on the Configure Search part of the installation (ElasticSeach) SELinux was also stopping things from working by denying permission to the server. For the sake of the installation I have temporarily disabled SELinux and will come back to it later...
Installation - current issue
After I disable SELinux and AtoM is successfully able to connect to the local ElasticSearch server I click on Save and Continue. This then takes hours and hours of the browser loading before eventually returning the attached error message. I have tried a clean installation three times resulting in the same outcome (sometimes takes less time, sometimes ages e.g. overnight before revealing the attached error message).
The error message, in brief, reports (also attached):
500 | Internal Server Error | PDOException
SQLSTATE[HY000]: General error: 2006 MySQL server has gone away
SQLSTATE[HY000]: General error: 2006 MySQL server has gone away
Naturally I did some looking around on this forum and found a few similar posts - not during installation, but same the same error message. I went to this one here and ended up on the AtoM Troubleshooting pages, before going to the MySQL v8.0 online documentation which then told me to try changing the wait_timeout. However this is already set to 8 hours - would the installation usually take this long? Furthermore, as advised in the AtoM Troubleshooting guide I tried starting MySQL with --log-warnings=2 enabled however this option was deprecated in MySQL v8. The new --verbose feature (without testing it) seems to imply it is for command line SQL logging...?
It has populated the database tables/structure, however now if I go to the web root now I get a blank page (with blank source code also).
Anyway, I'm a little stuck/lost as to what to try now so would grately appreciate any help from anyone who can point me in the right direction and help me through this installation. I have full access to the server to be able to make any required configuration changes. Appreciate I may need to start a clean installation again.
Many thanks in advance,
Stephen
Dan Gillean
Mar 31, 2020, 11:30:42 AM3/31/20
to ICA-AtoM Users
Hi Stephen,
Welcome to the AtoM community!
A couple of things that might help - please note I'm not a developer or a system administrator, but I can draw on the expertise of our team at Artefactual if my initial suggestions don't help you move forward. At the same time, I must warn you that our ability to support installations on different operating systems is limited - we test and develop against Ubuntu LTS releases, and the packages and libraries available on different distributions may not always match up with what we use in our recommended installation instructions.
In any case, we do have some community-generated guides on installing AtoM using CentOS on our wiki, that might help:
One important factor that I suspect is leading to some of the errors you are seeing: AtoM 2.5.x does not currently work with MySQL 8! The upcoming 2.6 release will work with MySQL 8 and we are introducing a lot of performance enhancements based on some of the new options available in that release, but for AtoM 2.5, you will probably want to downgrade to MySQL 5.7. You can see all the code changes we had to make in AtoM to ensure that MySQL 8 will work with 2.6 here, if you're curious:
In terms of Elasticsearch: AtoM 2.5 expects ES v5.6 - if you've installed later versions of ES, then again I would expect there to be issues. In most cases, problems with ES installation tend to be related to available memory - ES seems to require a lot of memory during installation. Here are some previous threads useful for troubleshooting Elasticsearch:
Finally, I wanted to make you aware of one more known issue with timeouts during installation involving the web installer. We're working on resolving this for 2.6, but in the meantime there are a couple of workaround options to try - see this thread:
We're tracking this issue and hope to include a more permanent fix in a future release, via this issue ticket:Hopefully these suggestions, and the CentOS guides on the wiki, will help you move forward. Please let us know how it goes!
Cheers,
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/aad157e8-0e3a-4d18-bd35-40133a241cfa%40googlegroups.com.
Message has been deleted
Stephen Harding
Apr 2, 2020, 11:41:52 AM4/2/20
to AtoM Users
Hi Dan,
With huge thanks to yourself pointing me in the right directions and also to the community (especially the author of the Centos guide) I've managed to successfully install AtoM.
Fixed earlier issued with ElasticSearch: I was stuck with an ElasticSeach error "permission denied" which I suppressed by disabling SELinux (not ideal). I was able to fix this using setsebool -P httpd_can_network_connect 1. I also hit an issue of the elasticsearch service crashing as soon as started, to overcome this I removed it, cleared /var/lib/elasticsearch, and reinstalled.
I then took the opportunity to rethink my software choices and took the
decision go with Nginx and MariaDB to ensure maximum compatibility and
support from the forum and documentation.
A clean install got me to the same place before (after clicking Save and Continue on Configure Search) loading for a while before crashing out but this time with a nginx 504 Timeout error. This is different to the message I had before (as I'm now using different version of MySQL). I looked at the thread you pointed me to where option 1 (changing the URL) didn't work so I did option 2 - setting fastcgi_read_timeout 120 then a clean install from scratch did the trick. I was then able to complete the install.
Thanks again for your support, no doubt I'll be back as I get to grips (or not!) with the system.
In fact one last question, can I just ask about Symfony? It's mentioned all over the forums and documentation and I understand that it's a PHP framework on which AtoM is developed in. However it is not mentioned anywhere as a required package to install and I'm unable to run any symfony comamnds on my server? Can you advise? I first stumbled upon it when reading this thread to create clean URLs by updating a Symfony config file and clearing the Symfony cache.
Thanks again,
StephenTo unsubscribe from this group and stop receiving emails from it, send an email to ica-ato...@googlegroups.com.
Dan Gillean
Apr 2, 2020, 12:50:06 PM4/2/20
to ICA-AtoM Users
Hi Stephen,
I'm glad you've managed to make progress! I appreciate you sharing what you did to get things working as well - hopefully this might help other users in the future. We're hoping to fix the web installer timeout issues in our 2.6 release, so hopefully this will get better in the future.
Regarding Symfony: there is no need to download or install it as a separate dependency, because everything you need is included in the AtoM code (so, depending on how you installed, it's included in the tarball you downloaded from our website, and/or in the AtoM code repository on GitHub.
All command-line tasks in AtoM that start with php symfony have to be run from AtoM's root installation directory to work - if you're using Nginx now and have tried wherever possible to follow our recommended installation instructions, this is typically /usr/share/nginx/atom, but it may be different in your environment. Typically, if you try to run Symfony commands anywhere else, you'll get a message like this:
- Could not open input file: symfony
If you're trying to run the commands from AtoM's root installation directory and it's still not working, it may be a permissions issue. When you follow our recommended installation instructions, all necessary permissions are assigned to the www-data user - if that's the case in your installation as well, you could always try specifying the user when you run commands, like so:
- sudo -u www-data php symfony search:populate
We've got a slide deck that introduces some of AtoM's command-line tasks here, that might provide a bit more context:
You'll also find a lot more tasks here:
Hope this helps!
he / him
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/6cb53a33-674e-45ad-8f5a-3967b7c2e395%40googlegroups.com.
Reply all
Reply to author
Forward
0 new messages