Installation problems

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tba...@gmail.com

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Apr 9, 2018, 3:14:08 AM4/9/18
to AtoM Users
Hi,

I'm completely new to AtoM,,but have some experience wtth dynamic web systems.
The installation went fine until the process hitthe elastic search installation which resulted in :

Fatal error: Allowed memory size of 134217728 bytes exhausted (tried to allocate 153545 bytes) in /home/hracag/web/atom/vendor/symfony/lib/i18n/sfMessageSource.class.php on line 199
http://203.14.158.10/index.php/sfInstallPlugin/configureSearch

Using this advice I increased the php memory limit to 1024Mb and restarted apache.

Attempting to load the elastic search install page resulted in the system hanging completely.

Now not sure what to do next - should I recommence the installation, or should I wipe the database entirely and start again.

Thanks
Tony

Dan Gillean

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Apr 9, 2018, 12:16:12 PM4/9/18
to ICA-AtoM Users
Hi Tony, 

You're on the right track! You might need to restart PHP-FPM (and memcached) for the changes to take effect. We have more information on adjusting PHP execution limits in our docs here: 
For example, you could also try adjusting the max_execution_time value as well - you can probably change it back after the installation completes, but it's true that Elasticsearch requires a lot of system memory for the installation. Once you've made your changes and restarted all services, I would try starting at the beginning of the web installer, rather than redoing the entire installation. You should be able to do this by returning to: 
Let us know how it goes! 

Cheers, 

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

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tba...@gmail.com

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Apr 10, 2018, 3:12:52 AM4/10/18
to AtoM Users
Thanks Dean,

I doubled the PHP exectuin limits to 60s.
Not sure on your link as only part was highlighted, so I restarted the process at:

    http://203.14.158.10/index.php/sfInstallPlugin/checkSystem

Worked OK until
   
    http://203.14.158.10/index.php/sfInstallPlugin/configureSearch

On hitting the accept button my browser displayed:

    Waiting for 203.14.158.10

For well over 5 minutes

The apache error log shows repeated entries:

[Tue Apr 10 15:19:13.004490 2018] [:error] [pid 28515] [client 203.14.158.61:33024] Empty module and/or action after parsing the URL "/" (/).
[Tue Apr 10 15:19:13.013895 2018] [:error] [pid 28515] [client 203.14.158.61:33024] PHP Fatal error:  Uncaught exception 'PDOException' with message 'SQLSTATE[42S02]: Base table or view not found: 1146 Table 'atom.setting' doesn't exist' in /home/hracag/web/atom/lib/QubitPdo.class.php:95\nStack trace:\n#0 /home/hracag/web/atom/lib/QubitPdo.class.php(95): PDOStatement->execute(Array)\n#1 /home/hracag/web/atom/lib/QubitPdo.class.php(35): QubitPdo::prepareAndExecute('SELECT?        ...', Array)\n#2 /home/hracag/web/atom/lib/model/QubitSetting.php(90): QubitPdo::fetchAll('SELECT?        ...', Array)\n#3 /home/hracag/web/atom/lib/filter/QubitSettingsFilter.class.php(34): QubitSetting::getSettingsArray()\n#4 /home/hracag/web/atom/cache/qubit/prod/config/config_core_compile.yml.php(1045): QubitSettingsFilter->execute(Object(sfFilterChain))\n#5 /home/hracag/web/atom/cache/qubit/prod/config/config_core_compile.yml.php(1009): sfFilterChain->execute()\n#6 /home/hracag/web/atom/cache/qubit/prod/config/config_core_compile.yml.php(1045): sfRenderingFilter->execute(Object(sfFilterChain))\n#7 /home/hracag/web/atom/plugins/sfHistoryPl in /home/hracag/web/atom/lib/QubitPdo.class.php on line 95

The databse shows 58 tables installed, including a table named "setting"
"select * from setting" did not elicit a response, althouhgh examining other tables showed most to be empty
None of the tables were marked as in use or locked.

Perhaps the database is corrupt, and I should wipe it, although I'm not sure whether any php files have been affected.
Any advice would be much appreciated.

Thanks
Tony

Dan Gillean

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Apr 10, 2018, 10:50:07 AM4/10/18
to ICA-AtoM Users
Hi Tony, 

You mentioned using Apache, rather than Nginx as we recommend. Can you tell me more about your installation environment? Are you using Ubuntu or something else? If Ubuntu, did you follow the 16.04 or 14.04 instructions? What version of PHP are you using, and what version of MySQL?

I have seen somewhat similar errors in the past when users install MySQL 5.7 - by default, strict mode is enabled in v5.7, and this can cause installation issues in AtoM. That might be something to check. 

Are you loading data, or working with a clean installation? Either way, I think that purging your data, and trying to run the SQL upgrade task to make sure your database schema version is correct might help. Let's try a few things. 

First, if you do have data, please be sure to make a backup first! This following command will purge everything in your database - as with all of these commands, it should be run from the root AtoM installation directory: 
  • php symfony tools:purge
The CLI prompt will walk you through the steps of naming the site and creating a new Admin user once the data is purged. Now to be sure, let's drop and recreate the AtoM database. Be sure to add your MySQL username and password to the following, as well as the name of your database where it says "new_database" - if you've followed our instructions up until now, your database is likely named atom:  
  • mysql -u username -pPASSWORD -e 'drop database new_database; create database new_database character set utf8 collate utf8_unicode_ci;'
If you do have data, now would be the time to load it back in to your new AtoM DB. 

Now we'll try running the SQL upgrade task to make sure you are on the correct schema version for your target installation: 
  • php symfony tools:upgrade-sql
If you are trying to install version 2.4, then the database version should be 156. 

If this doesn't resolve the issues, and you're not loading previous data, then .... I'm not sure why or where or how, but something has gone wrong in your installation. It could be a missing dependency, or an incorrect version of a dependency. I would suggest starting a fresh installation, and double-checking that you have all the required PHP extensions and additional dependencies installed. If you are using a different operating system than Ubuntu as your base, it's extra important to check the versions of any dependencies and their installation source - not all Linux distributions install the same packages from the same sources by default. 

If you are loading older AtoM data into your database, and you're still getting this error, then it may suggest that there's data corruption. The following guide should get you started in investigating: 


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

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Tony

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Apr 17, 2018, 1:07:53 AM4/17/18
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Thanks for your help, Dan

I followed your advice below, which resulted in further error.

This is a completely new installation, so I decided to wipe both the
files and database and start again.

That worked - AtoM is now installed and running OK.

I did note that installation of the elastic search component took quite
some time - a bit over 2 1/2 minutes in my case.

Thanks again
Tony



On 11/04/18 00:19, Dan Gillean wrote:
> Hi Tony,
>
> You mentioned using Apache, rather than Nginx as we recommend. Can you
> tell me more about your installation environment? Are you using Ubuntu
> or something else? If Ubuntu, did you follow the 16.04 or 14.04
> instructions? What version of PHP are you using, and what version of MySQL?
>
> I have seen somewhat similar errors in the past when users install MySQL
> 5.7 - by default, strict mode is enabled in v5.7, and this can cause
> installation issues in AtoM. That might be something to check.
>
> Are you loading data, or working with a clean installation? Either way,
> I think that purging your data, and trying to run the SQL upgrade task
> to make sure your database schema version is correct might help. Let's
> try a few things.
>
> First, if you do have data, please be sure to make a backup first! This
> following command will purge *everything* in your database - as with all
> of these commands, it should be run from the root AtoM installation
> directory:
>
> * php symfony tools:purge
>
> The CLI prompt will walk you through the steps of naming the site and
> creating a new Admin user once the data is purged. Now to be sure, let's
> drop and recreate the AtoM database. Be sure to add your MySQL username
> and password to the following, as well as the name of your database
> where it says "new_database" - if you've followed our instructions up
> until now, your database is likely named atom:
>
> * mysql -u username -pPASSWORD -e 'drop database new_database; create
> database new_database character set utf8 collate utf8_unicode_ci;'
>
> If you do have data, now would be the time to load it back in to your
> new AtoM DB.
>
> Now we'll try running the SQL upgrade task to make sure you are on the
> correct schema version for your target installation:
>
> * php symfony tools:upgrade-sql
>
> If you are trying to install version 2.4, then the database version
> should be 156.
>
> If this doesn't resolve the issues, and you're not loading previous
> data, then .... I'm not sure why or where or how, but something has gone
> wrong in your installation. It could be a missing dependency, or an
> incorrect version of a dependency. I would suggest starting a fresh
> installation, and double-checking that you have all the required PHP
> extensions and additional dependencies installed. If you are using a
> different operating system than Ubuntu as your base, it's extra
> important to check the versions of any dependencies and their
> installation source - not all Linux distributions install the same
> packages from the same sources by default.
>
> If you are loading older AtoM data into your database, and you're still
> getting this error, then it may suggest that there's data corruption.
> The following guide should get you started in investigating:
>
> * https://www.accesstomemory.org/docs/2.5/admin-manual/maintenance/troubleshooting/#dealing-with-data-corruption
>
> Good luck, and please let us know how it goes!
>
>
> Dan Gillean, MAS, MLIS
> AtoM Program Manager
> Artefactual Systems, Inc <http://www.artefactual.com/>.
> 604-527-2056
> @accesstomemory <https://twitter.com/accesstomemory>
>
> On Tue, Apr 10, 2018 at 3:12 AM, <tba...@gmail.com
> <mailto:tba...@gmail.com>> wrote:
>
> Thanks Dean,
>
> I doubled the PHP exectuin limits to 60s.
> Not sure on your link as only part was highlighted, so I restarted
> the process at:
>
> http://203.14.158.10/index.php/sfInstallPlugin/checkSystem
> <http://203.14.158.10/index.php/sfInstallPlugin/checkSystem>
>
> Worked OK until
>
> http://203.14.158.10/index.php/sfInstallPlugin/configureSearch
> <http://203.14.158.10/index.php/sfInstallPlugin/configureSearch>
>
> On hitting the accept button my browser displayed:
>
>     Waiting for 203.14.158.10
>
> For well over 5 minutes
>
> The apache error log shows repeated entries:
>
> [Tue Apr 10 15:19:13.004490 2018] [:error] [pid 28515] [client
> 203.14.158.61:33024 <http://203.14.158.61:33024>] Empty module
> and/or action after parsing the URL "/" (/).
> [Tue Apr 10 15:19:13.013895 2018] [:error] [pid 28515] [client
> 203.14.158.61:33024 <http://203.14.158.61:33024>] PHP Fatal error:
> <mailto:tba...@gmail.com> wrote:
>
> Hi,
>
> I'm completely new to AtoM,,but have some experience wtth
> dynamic web systems.
> The installation went fine until the process hitthe elastic
> search installation which resulted in :
>
> Fatal error: Allowed memory size of 134217728 bytes exhausted
> (tried to allocate 153545 bytes) in
> /home/hracag/web/atom/vendor/symfony/lib/i18n/sfMessageSource.class.php
> on line 199
> http://203.14.158.10/index.php/sfInstallPlugin/configureSearch
> <http://203.14.158.10/index.php/sfInstallPlugin/configureSearch>
>
> Using this advice
> <https://groups.google.com/forum/#!searchin/ica-atom-users/$2Fatom$2Fvendor$2Fsymfony$2Flib$2Fi18n$2FsfMessageSource.class.php$20on$20line$20199%7Csort:date/ica-atom-users/KFv-HceYbkI/Xwx52p9MAAAJ>
> I increased the php memory limit to 1024Mb and restarted apache.
>
> Attempting to load the elastic search install page resulted in
> the system hanging completely.
>
> Now not sure what to do next - should I recommence the
> installation, or should I wipe the database entirely and start
> again.
>
> Thanks
> Tony
>
> --
> 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
> <mailto:ica-atom-user...@googlegroups.com>.
> To post to this group, send email to ica-ato...@googlegroups.com
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> Visit this group at https://groups.google.com/group/ica-atom-users
> <https://groups.google.com/group/ica-atom-users>.
> To view this discussion on the web visit
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>
> For more options, visit https://groups.google.com/d/optout
> <https://groups.google.com/d/optout>.
>
>
> --
> You received this message because you are subscribed to the Google
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> To view this discussion on the web visit
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> <https://groups.google.com/d/msgid/ica-atom-users/CAC1FhZJQth2hWqBMRUgdb9iNUHRJCRqFAmVHNumNMTr9oNDD%2Bg%40mail.gmail.com?utm_medium=email&utm_source=footer>.

Dan Gillean

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Apr 17, 2018, 12:10:56 PM4/17/18
to ICA-AtoM Users
I'm glad to hear you've gotten it working, Tony! Thanks for updating the thread to let us know. Elasticsearch is a bit of a beast to get installed, it's true, but the hardest part is now complete! 

Cheers, 

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


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