Database upgrade from 2.4.7.1 to 2.4.8.1 generates Internal Server error

When doing the database upgrade from 2.4.7.1 to 2.4.8.1 from the web, we receive the following error message. Tried a couple of times and same error occurs. Yes, I turned installed=off to get to the page. Turned installed=on after failure and system seems to run fine. Suggestions? Is this also a max execution time? This is on a VPS so max execution time should not be an issue as in a shared host. Thank you.

Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator to inform of the time the error occurred and of anything you might have done that may have caused the error.

More information about this error may be available in the server error log

Is this a problem? php 5.3.3-40.el6_6

Hi @radjr,

Did you check your server’s PHP error log?

Regards,
Alec Smecher
Public Knowledge Project Team

No I did not. Will check. Interestingly, OJS still reporting that the upgrade needs to be done. I did do the test install first and it ran to completion.

Hi @radjr,

If the version number still reports as your old version, it suggests that the upgrade didn’t complete. One of the final steps is to update the version number in the DB. Your error log, I suspect, will contain some useful information.

Regards,
Alec Smecher
Public Knowledge Project Team

Thanks. I ran the update and it failed at the database upgrade. For us nubies, where was that log file? Sorry Friday Afternoon !

Hi @radjr,

The location of your PHP error log will depend on your hosting provider’s configuration, but usually it’s a file called error_log somewhere within your account.

Regards,
Alec Smecher
Public Knowledge Project Team

Won’t the extended PHP information link point to it?

Hi @radjr,

It may, but not necessarily. If PHP is configured to log errors through the web server, it’ll be up to the web server (e.g. Apache) to find the appropriate place to log the messages; that’s beyond PHP’s configuration.

Regards,
Alec Smecher
Public Knowledge Project Team

Look like the logs? What am I looking for? Thank you.
access_log error_log ssl_access_log suexec_log-20170108
access_log-20170108 error_log-20170108 ssl_error_log suexec_log-20170115
access_log-20170115 error_log-20170115 ssl_error_log-20130310 suexec_log-20170122
access_log-20170122 error_log-20170122 ssl_request_log suexec_log-20170129
access_log-20170129 error_log-20170129 suexec_log

Hi @radjr,

It’s likely the error_log file in that listing.

Regards,
Alec Smecher
Public Knowledge Project Team

All I see in the error_log file with the appropriate date/
/bin/tar: Removing leading /' from member names /bin/tar: -: Wrote only 2048 of 10240 bytes /bin/tar: Error is not recoverable: exiting now /bin/tar: Removing leading /’ from member names
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/locale/en_US/reader.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/locale/zh_CN/manager.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/locale/ru_RU/grid.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/locale/ru_RU/submission.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/crossref/locale/ca_ES/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/crossref/locale/id_ID/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/crossref/locale/da_DK/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/crossref/locale/ru_RU/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/crossref/PKPCrossrefCitationLookupPlugin.inc.php.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/isbndb/locale/ca_ES/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/isbndb/locale/id_ID/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/isbndb/locale/da_DK/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/isbndb/locale/ru_RU/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/isbndb/PKPIsbndbCitationLookupPlugin.inc.php.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/worldcat/locale/ca_ES/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/worldcat/locale/id_ID/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/worldcat/locale/da_DK/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/worldcat/locale/ru_RU/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/pubmed/locale/ca_ES/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/pubmed/locale/id_ID/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/pubmed/locale/da_DK/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/pubmed/locale/ru_RU/locale.xml.rej: Cannot open: Permission denied
/bin/tar: /var/www/vhosts/wmpllc.org/httpdocs/ojs-2.4.2/lib/pkp/plugins/citationLookup/pubmed/PKPPubmedCitationLookupPlugin.inc.php.rej: Cannot open: Permission denied
/bin/tar: Exiting with failure status due to previous errors
[Fri Jan 20 19:20:37 2017] [warn] mod_fcgid: process 7721 graceful kill fail, sending SIGKILL
[Fri Jan 20 19:21:41 2017] [warn] mod_fcgid: process 7733 graceful kill fail, sending SIGKILL
[Fri Jan 20 19:24:29 2017] [warn] mod_fcgid: process 7769 graceful kill fail, sending SIGKILL

Hi @radjr,

Those SIGKILL messages suggest a possible Apache timeout to me. I’d suggest checking your Apache configuration to see whether there’s a hard limit (e.g. 30 seconds).

Another option would be to run the upgrade again, then check the log immediately to see if a new message has been added. It’s hard to know from your log how long those messages have been there (beyond the few that do have timestamps).

Regards,
Alec Smecher
Public Knowledge Project Team

Understood. Thanks. You are the best!

Alec, this was hard coded as Timeout 60. But you would think that it should be enough? I have changed to 120. Will check to see if it runs. Is there an issue with a longer timeout? This would be a per session timeout correct? Thank you.

And I presume this is different than the KeepAlive timeout which is coded for 15 seconds.

Hi @radjr,

Depending on how much data you’re running through the upgrade, and the specifics of your server, it may indeed take longer than 60 seconds. If you suspect a timeout, try timing the upgrade with a watch to see if the process stops at a round number.

Regards,
Alec Smecher
Public Knowledge Project Team

Tried timeouts set at 480 seconds and it still fails around 60 seconds. I reread this not on the install page. Am I looking in the wrong place? Not HTTPF.CONF but PHP.INI??

please ensure that the max_execution_time directive in your php.ini configuration file is set to a high limit. If this or any other time limit (e.g. Apache’s “Timeout” directive) is reached and the upgrade process is interrupted, manual intervention will be required.

Changed max execution time from 60 to 480, still fails at 60. Does the daemon need to be restarted or something to reload the values?

Hi @radjr,

Yes, typically you’ll have to restart your Apache service in order for configuration changes to take effect.

Regards,
Alec Smecher
Public Knowledge Project Team