Atom 2.5 error FastCGI sent in stderr: "PHP message: No connection information ...

[Roberto JR]

Hello.

Trying to install atom 2.5 on ubuntu 16 and on 18 got the same error:

[error] 71539#71539: *1 FastCGI sent in stderr: "PHP message: No connection information in your runtime configuration file for datasource [propel]" while reading response header from upstream, client: 192.168.188.1, server: _, request: "GET / HTTP/1.1", upstream: "fastcgi://unix:/run/php7.0-fpm.atom.sock:", host: "192.168.188.152"

2019/05/11 10:59:16 

[error] 71539#71539: *7 upstream timed out (110: Connection timed out) while reading response header from upstream, client: 192.168.188.1, server: _, request: "GET /index.php/sfInstallPlugin/loadData HTTP/1.1", upstream: "fastcgi://unix:/run/php7.0-fpm.atom.sock", host: "192.168.188.152", referrer: "http://192.168.188.152/index.php/sfInstallPlugin/configureSearch"

What´s wrong?

Thanks

[Dan Gillean]

Hi Roberto, 

Can you tell us a bit more about where and how you got this error message? At what step of the installation process was this? Did you get to the web installer, and enter the proper configuration details? Did you notice that we recommend PHP 7.2 for the Ubuntu 18.04 installations? Did you install all the necessary PHP extensions described here, along with the PHP pool? Did you enable and start PHP-FPM after? What were you doing when you got this error? Etc. 

Any further info you can provide to help us understand exactly what you did, and how you got this error message, will help us provide better suggestions! Thanks! 

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

@accesstomemory

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[Roberto JR]

Hello. Thanks for the feedback, 

Yes I followed the instructions correctly ("bit-by-bit" - including php 7.2 for 18 and 7 for 16 with all the extensions without any error in any versions). The error occurred (on both systems) after second step in web-installer -  http://<host>/index.php/sfInstallPlugin/checkSystem

(Note: I have version 2.4.1 functional and operating perfectly on another 16 ubuntu server)

Thanks again.

[[]]

R.J.R.

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[Dan Gillean]

Hi Roberto, 

Usually at this stage, the web installer is looking for the database credentials, which should have been added to a new configuration file, config/config.php, after filling out the first page of the web installer. 

You can check to see if this file is present, and if needed, you can edit the MySQL username and password stored there to ensure you have the right credentials. 

If there are present and the file seems well-formed, then before we do anything else, lets try simply clearing the application cache and restarting PHP-FPM. For Ubuntu 18.04 with PHP 7.2:

• php symfony cc
• sudo systemctl restart php7.2-fpm
• sudo systemctl restart memcached

Remember to clear your browser cache after as well!. You should then be able to return to the web installer and ensure the credentials are correct, and proceed from there. If you need to return to the web installer, try navigating to [your site's base URL]/sfInstallPlugin/checkSystem

If that doesn't work, you can also delete the config/config.php file, and then return to the web installer. 

Let us know how it goes! 

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

@accesstomemory

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[Roberto JR]

Ok

I’ll try and return back the result soon

Thanks

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[Roberto JR]

Hello;

Unfortunately it did not work. The config/config.php file looks good, MySQL username and password seems ok, same error in web log and file

qubit_prod.log shows:

"symfony [crit] {PropelException} No connection information in your runtime configuration file for datasource [propel]"

I tested the database "atom" from mysql-console and it's ok.

I'try reinstall...

Thanks!

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[Roberto JR]

Hello.

I reinstalled both systems (16 and 18) following the instructions, but unfortunately the same error occurred again in both installations. It looks like some problem with connection to mysql, but I tested the database and it seemed ok.

Thanks

[Steve Breker]

Hi Roberto 

Is your mysql installed on a different server from where you are trying to install AtoM 2.5?  If so, you may need to allow access in mysql for the atom user / new server IP:

• mysql -u root -h localhost -p

• GRANT ALL ON atomdatabasename to atomuser@'new-atom-host-ip' IDENTIFIED BY 'atomuser';

• FLUSH PRIVILEGES;

If you do have a separate mysql server that you are connecting to and there is already a database called 'atom' present there (perhaps for another AtoM installation) make sure you name your new DB something unique!

Steve

[Roberto JR]

Hello Steve.

Thanks for the answer. 

MySql is installed on the same server. And I get access to the 'atom' database tables with the 'atom' user through mysql-console. Everything is ok. (wih ubuntu 16 and 18). I guess can be some kind of permission or some strict configuration.

Thanks

On Thu, May 16, 2019 at 2:53 PM Steve Breker <sbr...@artefactual.com> wrote:

Hi Roberto 

Is your mysql installed on a different server from where you are trying to install AtoM 2.5?  If so, you may need to allow access in mysql for the atom user / new server IP:

• mysql -u root -h localhost -p

• GRANT ALL ON *.* to root@'new-atom-host-ip' IDENTIFIED BY 'atomuser';

• FLUSH PRIVILEGES;

If you do have a separate mysql server that you are connecting to and there is already a database called 'atom' present there (perhaps for another AtoM installation) make sure you name your new DB something unique!

Steve

On Thursday, May 16, 2019 at 8:06:08 AM UTC-7, Roberto JR wrote:

Hello.

I reinstalled both systems (16 and 18) following the instructions, but unfortunately the same error occurred again in both installations. It looks like some problem with connection to mysql, but I tested the database and it seemed ok.

Thanks

On Mon, May 13, 2019 at 8:31 PM Roberto JR <rbr...@gmail.com> wrote:

Hello;

Unfortunately it did not work. The config/config.php file looks good, MySQL username and password seems ok, same error in web log and file

qubit_prod.log shows:

"symfony [crit] {PropelException} No connection information in your runtime configuration file for datasource [propel]"

I tested the database "atom" from mysql-console and it's ok.

I'try reinstall...

Thanks!

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[Steve Breker]

Hi Roberto

What value are you entering on the AtoM Configuration pages for "Database host"?

Reference:

https://www.accesstomemory.org/en/docs/2.5/admin-manual/installation/linux/ubuntu-xenial/#run-the-web-installer

Steve

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[Roberto JR]

Hello Steve,

This error appears in the first step of the installer,  "http://192.168.188.158/index.php/sfInstallPlugin/checkSystem"

[error] 26515#26515: *1 FastCGI sent in stderr: "PHP message: No connection information in your runtime configuration file for datasource [propel]" while reading response header from upstream, client: 192.168.188.1, server: _, request: "GET / HTTP/1.1", upstream: "fastcgi://unix:/run/php7.2-fpm.atom.sock:", host: "192.168.188.158"

(from "tail -f /var/log/nginx/error.log")

Thanks

R.J.R.

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[Roberto JR]

This error appears starting the first step of the installer,  "http://192.168.188.158/index.php/sfInstallPlugin/checkSystem"

Before enter values

Thanks..

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[Steve Breker]

Hi Roberto - After the errors occur do you see a "504 Gateway timeout" in your browser?

If so, after the timeout happens, if you alter the URI to be the root address (e.g. http://192.168.188.158 ) are you able to see the AtoM interface?

Steve

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[Steve Breker]

You might need to wait for approximately 20 seconds after the "504 timeout" before opening the root address (e.g. http://192.168.188.158 ).

[Roberto JR]

Hello Steve,

Thanks!

Well, Ok. Typing the address after the errors, the default atom interface appears, but the site configuration step is not shown and therefore it is not possible to create any account to use the service.

Note: the error "[error] 17665#17665: *1 FastCGI sent in stderr: "PHP message: No connection information in your runtime configuration ... " appears immediately after typing the address (step "/checkSystem") and the error "[error] 17665#17665: *10 upstream timed out (110: Connection timed out) ..." appear in the step "sfInstallPlugin/loadData"

weird... Isn´ it?

Thanks!

[Steve Breker]

Hi Roberto

I've been able to replicate your issue as you've described above. It appears it is possible for the install task that creates the database and Elasticsearch index to run for longer than 1 minute. The default duration for NGINX's fastcgi_read_timeout setting is 1 minute.

I think this particular piece of code may need to be broken up to lower the overall time it takes to run. I be creating a ticket to look into this.

There are two ways to work around this problem in the meantime:

A) The easiest way is to proceed with the next URI in the install process.

1. When the 504 error occurs the DB has been successfully created. When you see the 504 error in your browser the URI should look like: http://<host>/index.php/sfInstallPlugin/loadData
2. Change the URI to: http://<host>/index.php/sfInstallPlugin/configureSite and press the Enter key.
3. The last page in the install process will appear and you can complete the last steps of the installation.

B) Alternatively, it is also possible to edit the nginx fastcgi timeout value to increase the setting allowing the loaddata call to complete. This would have to be completed before running the AtoM Web installer. This is a riskier approach and requires editing the nginx atom config file.

Because the earlier workaround (A) is so easy, I cannot recommend making this change - doing this could have a negative impact on a large AtoM installation. In addition, once AtoM is successfully installed there is no longer any need for this setting to be set to this higher value.

1. If you followed the Artefactual install instructions you created the file /etc/nginx/sites-available/atom
2. Before running the web installer edit this file and add the line fastcgi_read_timeout 120;
3. It should be added in the section that begins (approx line 54):   location ~ ^/(index|qubit_dev)\.php(/|$) {

Steve

[Roberto JR]

Hi Steve,

Okay. I'll try these options that you have suggested and return as soon as possible.

Thanks!

[[]]

R.J.R.

On Thu, May 23, 2019 at 8:19 PM Steve Breker <sbr...@artefactual.com> wrote:

Hi Roberto

[Roberto JR]

Alo Steve. THanks!
I tried your suggestion of tha option (A) (twice to ensure success) and after a time> 20s I used the url "/index.php/sfInstallPlugin/configureSite". The configuration step has appeared and the configuration can be done entirely.
It is functional now (bur I did not loaded the backup for testing yet). But it is certainly that is a process that needs to be reviewed.

I´ll restore backup (data) and continue test all.
Thanks Steve for not giving up!

8D

[[]]

R.J.R.

On Thu, May 23, 2019 at 8:19 PM Steve Breker <sbr...@artefactual.com> wrote:

Hi Roberto

[Steve Breker]

Hi Roberto - I am very glad to hear that Option A worked for you.  You are correct - waiting about 20 second after the 504 error allows the task time to complete!

I have created a ticket for this issue: https://projects.artefactual.com/issues/13051

Thanks for your help in identifying this issue!

Steve

Steven Breker, BSc
AtoM Programmer
Artefactual Systems, Inc.
604-527-2056

[ronald...@gmail.com]

Hello everyone,

I had the same problems as Roberto Jr, I managed to overcome following plan A, but now I'm having problems after this stage where I do the initial configuration of the application and when I try to save I get the error:

 Oops! An Error Occurred

Sorry, something went wrong.

The server returned a 500 Internal Server Error.

Try again a little later or ask in the discussion group.

Back to previous page.

in logs (var / log / nginx / error.log)

displays the following msg:

PHP message: Unable to execute INSERT statement. [wrapped: SQLSTATE [23000]: Integrity constraint violation: 1452 Can not add or update child row: a foreign key constraint fails (`atom`.`acl_user_group`, CONSTRAINT` acl_user_group_FK_2` FOREIGN KEY (`group_id`) REFERENCES` acl_group` ('id`) ON DELETE CASCADE) "while reading response header from upstream, client: 10.1.12.45, server: _, request:" POST /index.php/sfInstallPlugin/configureSite HTTP / 1.1 ", upstream:" fastcgi: //unix:/run/php7.2-fpm.atom.sock: ", host:" 10.1.3.95 ", referrer:" http://10.1.3.95/index.php/sfInstallPlugin/configureSite

any tips?

Regards

Ronaldo Soares

[Dan Gillean]

Hi Ronaldo, 

Is this a 2.5.0 or 2.5.1 installation? Can you please also run the following command to check the database schema version, and share the output?

• php symfony tools:get-version

You should see output something like: 

/usr/share/nginx/atom$ php symfony tools:get-version

2.5.1 v172

If that command doesn't work you can check the database schema version in the database directly with a mysql client:

• select name,value from setting s join setting_i18n i18n on s.id = i18n.id where name='version';

The output of this SQL query should return something like the following: 

+---------+-------+
| name    | value |
+---------+-------+
| version | 172   |
+---------+-------+
1 row in set (0.00 sec)

For both 2.5.0 and 2.5.1, the database schema version should be v172. If yours is not 172 and you are using 2.5.x, this may mean that the Upgrade task was not properly run against your data during the upgrade process. See: 

• https://www.accesstomemory.org/docs/latest/admin-manual/installation/upgrading/#run-the-upgrade-task
  

This task runs several sequential scripts that will add, remove, or modify AtoM database tables and columns based on fixes and new features. If it is not at the correct version, this can sometimes lead to errors. 

Anything further you can tell us about your installation will also help. For example, I can see you are using PHP 7.2 - is this an Ubuntu 18.04 installation? Does your site have a custom theme, or any other code customizations? What is the default installation culture (i.e. language) you used during the installation? etc. 

Thanks! 

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

@accesstomemory

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[Matthew Bruton]

Dan,

I am trying the "get version" command you are recommending above and am getting the following error:

[wrapped: SQLSTATE[42S02]: Base table or view not found: 1146 Table 'atom.setting' doesn't exist]

Does this mean the database has not been created?

My problem is identical to the users above. I am trying to install the atom on another system with even better RAM.

Thanks,

Matthew

[Dan Gillean]

Hi Matthew, 

I would recommend trying the following steps to see if it helps. Please note, we are going to purge everything from your database, so you should definitely make sure you have a database backup if you have any data loaded first! The upgrade guide tells you how to back up the data. 

First, you can check if MySQL is installed, and what version you are running with the following: 

• sudo mysqladmin version
  

Assuming you have the correct version (v 5.7.x) already installed, first, make your backup if you haven't already. For example, assuming your database name is atom, and the username and password are both root, you could do the following to make a copy (called atom-backup.sql) in your /tmp directory: 

• mysqldump -u root -proot atom > /tmp/atom-backup.sql
  

Now, we will run the command to purge everything from the database. This is the step that deletes all your data, so don't proceed without making a backup first if you want to keep your data! Run the following from AtoM's root installation directory (which is typically /usr/share/nginx/atom if you followed our recommended installation instructions)

• php symfony tools:purge

AtoM will delete everything, and then walk you through the steps to name your site and add an admin user. If you are going to load a backup of your data back in after, don't worry about what credentials you enter here - they will be overwritten when we load the data back in by whatever is saved in your backup. 

Now, let's try dropping and recreating your database. Again, the example command below assumes that your database name is atom, and the username and password are both root - feel free to make changes to the command if you've used different credentials: 

• mysql -u root -proot -e 'drop database atom; create database atom character set utf8 collate utf8_unicode_ci;'
  

Now, you can load your data back in: 

• mysql -u root -proot atom < /tmp/atom-backup.sql
  

And then we'll try to run the upgrade task: 

• php symfony tools:upgrade

Let me know if that helps! 

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

@accesstomemory

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[johngr...@gmail.com]

Hi, I'm bravely trying to install Atom 2.5.3 on CentOS 8/Apache/MariaDB.

It was going well until I got the Gateway 504 error. Followed the steps above - my DB looks populated but now getting this in /var/log/php-fpm/www-error.log :

PHP Fatal error:  Uncaught PDOException: SQLSTATE[42S02]: Base table or view not found: 1146 Table 'atom.setting' doesn't exist in /var/www/html/atom-2.5.3/lib/QubitPdo.class.php:95
Stack trace:
#0 /var/www/html/atom-2.5.3/lib/QubitPdo.class.php(95): PDOStatement->execute()
#1 /var/www/html/atom-2.5.3/lib/QubitPdo.class.php(35): QubitPdo::prepareAndExecute()
#2 /var/www/html/atom-2.5.3/lib/model/QubitSetting.php(90): QubitPdo::fetchAll()
#3 /var/www/html/atom-2.5.3/lib/filter/QubitSettingsFilter.class.php(34): QubitSetting::getSettingsArray()
#4 /var/www/html/atom-2.5.3/cache/qubit/prod/config/config_core_compile.yml.php(1045): QubitSettingsFilter->execute()
#5 /var/www/html/atom-2.5.3/cache/qubit/prod/config/config_core_compile.yml.php(1009): sfFilterChain->execute()
#6 /var/www/html/atom-2.5.3/cache/qubit/prod/config/config_core_compile.yml.php(1045): sfRenderingFilter->execute()
#7 /var/www/html/atom-2.5.3/plugins/sfHistoryPlugin/lib/sfHistoryPluginFilter.class.php(18): sfFilterChain->execute()
#8 /var/www/html/atom-2.5.3/c in /var/www/html/atom-2.5.3/lib/QubitPdo.class.php on line 95

I do have a atom.setting table but it's called setting_i18n

Any ideas what to try next ?

PHP is 7.4 so a bit bleeding edge.

Cheers

Grant

[johngr...@gmail.com]

BTW, when i try :

php symfony tools:purge, here is the output :
[root@localhost atom-2.5.3]# php symfony tools:purge
>> schema    converting "/var/www/html/atom-2.5.3/config/schema.yml" to XML
>> schema    putting /var/www/html/atom-2.5.3/config/generated-schema.xml
>> schema    converting "/var/www/html/atom-2.5.3/plugins/qbAclPlugin/config/schema.yml" to XML
>> schema    putting /var/www/html/atom-2.5.3/plugins/qbAclPlugin/config/generated-qbAclPlugin-schema.xml
>> schema    converting "/var/www/html/atom-2.5.3/plugins/qtAccessionPlugin/config/schema.yml" to XML
>> schema    putting /var/www/html/atom-2.5.3/plugins/qtAccessionPlugin/config/generated-qtAccessionPlugin-schema.xml
>> file+     config/generated-qbAclPlugin-schema.xml
>> file-     /var/www/html/atom-2.5.3/plugins/qbAclPlugin/config/generated-qbAclPlugin-schema.xml
>> file+     config/generated-qtAccessionPlugin-schema.xml
>> file-     /var/www/html/atom-2.5.3/plugins/qtAccessionPlugin/config/generated-qtAccessionPlugin-schema.xml
                                                                   
  WARNING: The data in the database related to the connection name 
           propel will be removed.                                 
                                                                   
  Are you sure you want to proceed? (y/N)                          
                                                                   
y
>> propel    Running "insert-sql" phing task
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/system/io/UnixFileSystem.php on line 78
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/system/io/UnixFileSystem.php on line 79
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/system/io/UnixFileSystem.php on line 91
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/system/io/UnixFileSystem.php on line 112
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/system/io/UnixFileSystem.php on line 125
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/system/io/UnixFileSystem.php on line 143
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/system/io/UnixFileSystem.php on line 157
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/system/io/UnixFileSystem.php on line 197
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/tasks/system/CvsPassTask.php on line 144
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/tasks/system/PropertyTask.php on line 415
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/lib/Capsule.php on line 186
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/lib/Capsule.php on line 186
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/lib/Capsule.php on line 188
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/lib/Capsule.php on line 188
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/phing/lib/Capsule.php on line 188
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/propel-generator/classes/propel/engine/GeneratorConfig.php on line 122
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/propel-generator/classes/propel/engine/GeneratorConfig.php on line 122
PHP Deprecated:  Array and string offset access syntax with curly braces is deprecated in /var/www/html/atom-2.5.3/vendor/symfony/lib/plugins/sfPropelPlugin/lib/vendor/propel-generator/classes/propel/engine/database/transform/XmlToAppData.php on line 184
>> file-     /var/www/html/atom-2.5.3/config/generated-qtAccessionPlugin-schema.xml
>> file-     /var/www/html/atom-2.5.3/config/generated-qbAclPlugin-schema.xml
>> file-     /var/www/html/atom-2.5.3/config/generated-schema.xml

                                                  
  unknown key [number_of_shards] for create index 
                                                  

PHP Fatal error:  Uncaught Elastica\Exception\ResponseException: no such index [atom] [index: atom] in /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Transport/Http.php:179
Stack trace:
#0 /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Request.php(193): Elastica\Transport\Http->exec()
#1 /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Client.php(674): Elastica\Request->send()
#2 /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Client.php(706): Elastica\Client->request()
#3 /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Index.php(562): Elastica\Client->requestEndpoint()
#4 /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Index.php(250): Elastica\Index->requestEndpoint()
#5 /var/www/html/atom-2.5.3/plugins/arElasticSearchPlugin/lib/arElasticSearchPlugin.class.php(117): Elastica\Index->refresh()
#6 [internal function]: arElasticSearchPlugin->__destruct()
#7 {main}
  thrown in /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Transport/Http.php on line 179

Fatal error: Uncaught Elastica\Exception\ResponseException: no such index [atom] [index: atom] in /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Transport/Http.php:179
Stack trace:
#0 /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Request.php(193): Elastica\Transport\Http->exec()
#1 /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Client.php(674): Elastica\Request->send()
#2 /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Client.php(706): Elastica\Client->request()
#3 /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Index.php(562): Elastica\Client->requestEndpoint()
#4 /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Index.php(250): Elastica\Index->requestEndpoint()
#5 /var/www/html/atom-2.5.3/plugins/arElasticSearchPlugin/lib/arElasticSearchPlugin.class.php(117): Elastica\Index->refresh()
#6 [internal function]: arElasticSearchPlugin->__destruct()
#7 {main}
  thrown in /var/www/html/atom-2.5.3/vendor/elastica/Elastica/Transport/Http.php on line 179

[Dan Gillean]

Hi Grant, 

Thanks for sharing the output logs - and I can see you've already done some hunting around in the forum for possible solutions, which we always appreciate! 

I'm not sure it's the culprit here, but I will say that I expect you to run into issues with PHP 7.4 at some point. From what I recall, we saw some breaking changes in PHP 7.3 that were going to require some code updates in AtoM for full compatibility, and it's possible there are more in v7.4. If it is at all possible to downgrade to v7.2, I would recommend it for use with AtoM 2.5.3. 

In the same vein, what version of Elasticsearch are you using? AtoM 2.5.3 is confirmed with work with ES 5.6, but if you are trying to use ES 6 or higher, I suspect you will encounter issues. 

In terms of "trying the solutions above" which one(s) did you try? Did you try simply waiting a bit and advancing to the next page of the installer, or did you try adjusting the timeout limits in PHP and your webserver? For some users, adjusting the Nginx fastcgi_timeout value (as this user did) resolved the exact same exception - I don't know exactly what the equivalent would be in Apache, but that might something to look for?

Beyond this, I don't have further suggestions at the moment, so once I have a bit more information from you, I will consult with our developers to see if they have further ideas. 

Cheers, 

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

@accesstomemory

he / him

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[johngr...@gmail.com]

To get past the 504 error, I used the direct URL method, which brought up the configuration page /index.php/sfInstallPlugin/configureSite

When I submitted my data, I got the  500 error.

I did tweak some settings in php.ini to increase max_input_time, max_execution_time and memory_limit but that didn't stop the 504 error.

I will check what version of ES I'm using - I installed using the RPM.

Cheers

Grant

[Dan Gillean]

Hi Grant, 

Based on the off-forum message you sent me, it looks like you have the latest version (7.5.1) of Elasticsearch installed currently. As I mentioned in my initial reply, AtoM 2.5.3 is confirmed with work with ES 5.6, but if you are trying to use ES 6 or higher, I suspect you will encounter issues. 

I suggest that you downgrade ES as well as your PHP version - Elastic is very much a "move fast and break things" company, and they have introduced major breaking changes into both versions 6 and 7 of Elasticsearch that will require some code updates in AtoM for compatibility. 

I would recommend that you fully remove any other versions of ES first, and then install ES 5.6 from scratch. 

Based on a couple quick online searches, the following should completely uninstall the current version of ES in a default Ubuntu installation, including any config files and older indexes. You may need to do a bit more research for CentOS if it doesn't work: 

• sudo apt-get --purge autoremove elasticsearch
• sudo rm -rf /var/lib/elasticsearch
• sudo rm -rf /etc/elasticsearch
  

Then you can return to the section in our documentation on installing Elasticsearch and begin that part again. 

I suspect that, between the PHP version and the ES version, installing the correct version of dependencies will resolve the majority of your issues. While we are on the topic, note that the current highest version of MySQL/percona we recommed is version 5.7 - in the 2.6 release, we will be upgrading this dependency to MySQL8, but in version 2.5.x this is not yet supported. 

Note that though we do not officially support and maintain documentation for CentOS installs, one of our system administrators has previously shared an installation guide in a gist that might be of use: 

• https://gist.github.com/scollazo/7a13dbea3ea88f8d7463befa4e996d0d  
  

As well, you may wish to take a look at the other posts in the forum tagged with CentOS/RHEL - there have been several community-shared installation guides there as well: 

• https://groups.google.com/forum/#!tags/ica-atom-users/centOS  
  

Good luck! 

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

@accesstomemory

he / him

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[johngr...@gmail.com]

A quick update - abandoned trying to install on VMs, I get the impression that this project is quite resource-intensive so I have switched to a laptop with 8G of RAM, Ubuntu 19.10, ES 5.6.16, Nginx 1.16.1, PHP 7.0, MariaDB 10.3.20, Atom 2.5.3

First attempt - 504 gateway timeout, /var/log/nginx/error_log :

2020/01/16 23:27:27 [error] 14064#14064: *79 upstream timed out (110: Connection timed out) while reading response header from upstream, client: 127.0.0.1, server: atom.local, request: "GET /index.php/sfInstallPlugin/loadData HTTP/1.1", upstream: "fastcgi://unix:/run/php7.0-fpm.atom.sock", host: "atom.local", referrer: "http://atom.local/index.php/sfInstallPlugin/configureSearch"

Waited * a long time * until Atop showed MySql process < 5% CPU, HDD activity dropped.

Added {fastcgi_read_timeout 120;} to /etc/nginx/sites_available/atom

Increased [max_execution_time] in /etc/php/atom.conf to 240s
Restarted nginx and php7.0-fpm

Went to URL /index.php/sfInstallPlugin/configureSite

Waited some more..and some more...504 error again, eventually MySQL process CPU % began to drop.

Restarted nginx, php7.0-fpm and MariaDB

Re-loaded page - Bingo !

Success at the third attempt.

Now that I understand the resource-intensive nature, I'll go back to the CentOS guide and see if I can resurrect that one :)

Cheers

Grant

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