Internal Server Error occured when upgrading from OJS 2.3.8.0 to 2.4.8

Software Support
1

Hi,

I was trying to upgrade OJS 2.3.8.0 to 2.4.8 and got an Internal server error.

Please find the below error message and help me to figure out the problem and solve it.

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator at webmaster@xxxx.org to inform them of the time this error occurred, and the actions you performed just before this error.

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

Additionally, a 500 Internal Server Error error was encountered while trying to use an ErrorDocument to handle the request.

Current Php version : 5.4.45

Old php version : 5.3.29

Hosted at Godaddy.

2

Dear Alec,

Can you help me on this ?

It was working fine with the old version and godaddy updated php version, so its through some error. So I was updating the OJS to the new version. During upgrade it made the above error.

I checked the even log the database and it was 15501 and i tried to delete it but still the same count. So I restore the database from the back and tried again. But the result was same “Internal server error”.

Please help me on this.

Thanks in advance

Johnson K. Baby

3

Hi @sonbabyjohn,

Check your server’s PHP error log and web server error log (sometimes these are the same). A 500 error should indicate that there is more information in your error log.

Regards,
Alec Smecher
Public Knowledge Project Team

4

Hi @asmecher,

Thank you for the reply.

Please find the below log file.

80.184.88.32 - - [20/Jun/2016:10:51:44 -0700] “GET /jer/lib/pkp/js/lib/jquery/plugins/validate/jquery.validate.js HTTP/1.1” 200 9657 “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:51:57 -0700] “GET /jer/index.php/index/install/upgrade HTTP/1.1” 200 3644 “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:51:59 -0700] “GET /jer/lib/pkp/templates/images/icons/font-default.png HTTP/1.1” 200 3760 “http://iscienceworld.org/jer/index.php/index/install/upgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:51:59 -0700] “GET /jer/lib/pkp/templates/images/icons/font-up.png HTTP/1.1” 200 3879 “http://iscienceworld.org/jer/index.php/index/install/upgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:51:59 -0700] “GET /jer/lib/pkp/templates/images/icons/font-down.png HTTP/1.1” 200 3883 “http://iscienceworld.org/jer/index.php/index/install/upgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:52:04 -0700] “POST /jer/index.php/index/install/installUpgrade HTTP/1.1” 200 3759 “http://iscienceworld.org/jer/index.php/index/install/upgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:53:13 -0700] “GET /jer/index.php/index/install/upgrade HTTP/1.1” 200 3644 “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:53:53 -0700] “GET /info.php HTTP/1.1” 200 12609 “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:53:53 -0700] “GET /info.php?=PHPE9568F34-D428-11d2-A769-00AA001ACF42 HTTP/1.1” 200 2547 “http://iscienceworld.org/info.php” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:53:54 -0700] “GET /info.php?=PHPE9568F35-D428-11d2-A769-00AA001ACF42 HTTP/1.1” 200 2169 “http://iscienceworld.org/info.php” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:53:20 -0700] “POST /jer/index.php/index/install/installUpgrade HTTP/1.1” 404 - “http://iscienceworld.org/jer/index.php/index/install/upgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:55:44 -0700] “GET /jer/index.php/index/install/installUpgrade HTTP/1.1” 200 3768 “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:56:13 -0700] “GET /jer/ HTTP/1.1” 302 - “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:56:13 -0700] “GET /jer/index.php/index/install HTTP/1.1” 200 7555 “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:56:27 -0700] “GET /jer/index.php/index/install/upgrade HTTP/1.1” 200 3644 “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:56:41 -0700] “POST /jer/index.php/index/install/installUpgrade HTTP/1.1” 200 3768 “http://iscienceworld.org/jer/index.php/index/install/upgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:58:36 -0700] “GET /jer/lib/pkp/templates/images/icons/font-up.png HTTP/1.1” 304 - “http://iscienceworld.org/jer/index.php/index/install/installUpgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:58:36 -0700] “GET /jer/lib/pkp/templates/images/icons/font-default.png HTTP/1.1” 304 - “http://iscienceworld.org/jer/index.php/index/install/installUpgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:10:58:36 -0700] “GET /jer/lib/pkp/templates/images/icons/font-down.png HTTP/1.1” 304 - “http://iscienceworld.org/jer/index.php/index/install/installUpgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:21:12 -0700] “GET /jer/ HTTP/1.1” 302 - “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:21:13 -0700] “GET /jer/index.php/index/install HTTP/1.1” 200 7555 “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:21:14 -0700] “GET /jer/lib/pkp/styles/common.css HTTP/1.1” 304 - “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:21:14 -0700] “GET /jer/styles/common.css HTTP/1.1” 304 - “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:21:15 -0700] “GET /jer/lib/pkp/templates/images/icons/font-up.png HTTP/1.1” 304 - “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:21:15 -0700] “GET /jer/lib/pkp/templates/images/icons/font-default.png HTTP/1.1” 304 - “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:21:16 -0700] “GET /jer/lib/pkp/templates/images/icons/font-down.png HTTP/1.1” 304 - “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:21:18 -0700] “GET /jer/index.php/index/install/upgrade HTTP/1.1” 200 3644 “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:21:22 -0700] “POST /jer/index.php/index/install/installUpgrade HTTP/1.1” 404 - “http://iscienceworld.org/jer/index.php/index/install/upgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:24:14 -0700] “GET / HTTP/1.1” 302 - “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:42:47 -0700] “GET /jer/ HTTP/1.1” 302 - “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:42:48 -0700] “GET /jer/index.php/index/install HTTP/1.1” 200 7555 “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:42:49 -0700] “GET /jer/lib/pkp/templates/images/icons/font-default.png HTTP/1.1” 304 - “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:42:49 -0700] “GET /jer/lib/pkp/templates/images/icons/font-up.png HTTP/1.1” 304 - “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:42:49 -0700] “GET /jer/lib/pkp/templates/images/icons/font-down.png HTTP/1.1” 304 - “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:45:43 -0700] “GET /jer/index.php/index/install HTTP/1.1” 200 7555 “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:45:50 -0700] “GET /jer/index.php/index/install/upgrade HTTP/1.1” 200 3644 “http://iscienceworld.org/jer/index.php/index/install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:11:46:07 -0700] “POST /jer/index.php/index/install/installUpgrade HTTP/1.1” 404 - “http://iscienceworld.org/jer/index.php/index/install/upgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:12:01:42 -0700] “GET /jer/ HTTP/1.1” 302 - “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:12:01:42 -0700] “GET /jer/index.php?journal=index&page=install HTTP/1.1” 200 7601 “-” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:12:01:49 -0700] “GET /jer/index.php?journal=index&page=install&op=upgrade HTTP/1.1” 200 3691 “http://iscienceworld.org/jer/index.php?journal=index&page=install” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”
80.184.88.32 - - [20/Jun/2016:12:01:53 -0700] “POST /jer/index.php?journal=index&page=install&op=installUpgrade HTTP/1.1” 404 - “http://iscienceworld.org/jer/index.php?journal=index&page=install&op=upgrade” “Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36”

Please try to help me …

Thank you,
Johnson K. Baby

5

Hi @sonbabyjohn,

That appears to be your access log, not your error log.

Regards,
Alec Smecher
Public Knowledge Project Team

6

Hi @asmecher,

This is what I could find. I cannot find any error log file in the godaddy shared server.

Thank you,

Johnson K. Baby

7

Hi @sonbabyjohn,

Unfortunately I can’t help debug this without the error message.

Regards,
Alec Smecher
Public Knowledge Project Team

9

Hi @asmecher,

At last I could generate the error log which is below.

[21-Jun-2016 19:10:50 UTC] ojs2 has produced an error
Message: WARNING: date(): It is not safe to rely on the system’s timezone settings. You are required to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected the timezone ‘UTC’ for now, but please set date.timezone to select your timezone.
In file: /home/mysite/public_html/jer/lib/pkp/classes/core/Core.inc.php
At line: 95
Stacktrace:
Server info:
OS: Linux
PHP Version: 5.4.45
Apache Version: N/A
DB Driver: mysql
[21-Jun-2016 19:10:50 UTC] ojs2 has produced an error
Message: WARNING: Cannot modify header information - headers already sent by (output started at /home/mysite/public_html/jer/lib/pkp/classes/core/PKPApplication.inc.php:384)
In file: /home/mysite/public_html/jer/lib/pkp/classes/template/PKPTemplateManager.inc.php
At line: 340
Stacktrace:
Server info:
OS: Linux
PHP Version: 5.4.45
Apache Version: N/A
DB Driver: mysql
[21-Jun-2016 19:10:50 UTC] ojs2 has produced an error
Message: WARNING: Cannot modify header information - headers already sent by (output started at /home/mysite/public_html/jer/lib/pkp/classes/core/PKPApplication.inc.php:384)
In file: /home/mysite/public_html/jer/lib/pkp/classes/template/PKPTemplateManager.inc.php
At line: 343
Stacktrace:
Server info:
OS: Linux
PHP Version: 5.4.45
Apache Version: N/A
DB Driver: mysql
[21-Jun-2016 19:15:34 UTC] ojs2 has produced an error
Message: WARNING: date(): It is not safe to rely on the system’s timezone settings. You are required to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected the timezone ‘UTC’ for now, but please set date.timezone to select your timezone.
In file: /home/mysite/public_html/jer/lib/pkp/classes/core/Core.inc.php
At line: 95
Stacktrace:
Server info:
OS: Linux
PHP Version: 5.4.45
Apache Version: N/A
DB Driver: mysql
[21-Jun-2016 19:15:40 UTC] ojs2 has produced an error
Message: WARNING: date(): It is not safe to rely on the system’s timezone settings. You are required to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected the timezone ‘UTC’ for now, but please set date.timezone to select your timezone.
In file: /home/mysite/public_html/jer/lib/pkp/classes/core/Core.inc.php
At line: 95
Stacktrace:
Server info:
OS: Linux
PHP Version: 5.4.45
Apache Version: N/A
DB Driver: mysql
[21-Jun-2016 19:17:46 UTC] ojs2 has produced an error
Message: WARNING: date(): It is not safe to rely on the system’s timezone settings. You are required to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected the timezone ‘UTC’ for now, but please set date.timezone to select your timezone.
In file: /home/mysite/public_html/jer/lib/pkp/classes/core/Core.inc.php
At line: 95
Stacktrace:
Server info:
OS: Linux
PHP Version: 5.4.45
Apache Version: N/A
DB Driver: mysql

Please try to figure out the problem.

Thank you,

Johnson K. Baby

10

There should be a different line in the error log that references a “FATAL” error, as opposed to the above “WARNING” messages.

If you follow the instructions in those warnings and provide a date.timezone setting in your PHP configuration, your error log will be a lot cleaner and it will be easier to find the fatal error.

11

Hi @asmecher & @ctgraham,

Thank you for the support you are providing to overcome my problem.

I think my problem upgrade is with the max_execution_time of my shared server with the godaddy. I can see the max_execution _time from the php info file is that 600. But when I run the upgrade its getting exit after 2 mins with 500 internal server error. I think even if the max_execution_time is 600, it exits at 120. Can you give me a solution on this ? or any other alternative method ?

Thanks in advance,

Johnson K. Baby

12

That sounds like a good theory. Check with your hosting provider to see if there are other system or service settings which might be terminating the process after 120 seconds.

13

Hi @asmecher & @ctgraham,

The problem is not yet resolved.

The php is not running in safe mode, then will it affect the max_execution_time when we do OJS upgrade ?

I increased the max_execution_time in php.ini file and it reflects in info.php to 600 still it give 500 internal server error.

I checked the error log as well and nothing mentioned in it in this regard.

What could be the reason, and is there any other alternative to manage ?

Thank you,
Johnson K. Baby

14

Did you check with your hosting provide regarding increasing the max_execution_time? If PHP is running in safe mode, your modification to the max_execution_time may be ignored. This will depend on the hosting provider’s configuration, and they should be able to assist.

If you have shell access to the machine, this can all easily be worked around by running the upgrade via command line instead of via the web interface. There is no max_execution_time from the command line (CLI).

15

Dear @ctgraham & @asmecher,

Perfect … Its worked out.

I could successfully upgrade from 2.3.8 to 2.4.8 without any issues using shell access and command line interface.

You buddies are awesome …

Once again Thank you,

Johnson K. Baby