Lost electricity during upgrading Ubuntu 16.04.1

Hi,

I'm upgrading my server from Ubuntu 14.04 to 16.0.4.1 following the guidelines here: https://www.virtualmin.com/documentation/system/os/ubuntu-trusty-to-xenial However, my PC (not server) was shutdown and when I SSH to my server again, it already show the Ubuntu 16.0.4.1 OS. Now I cannot use apt-get update because of the follow error:

W: No sandbox user '_apt' on the system, can not drop privileges
E: Could not get lock /var/lib/dpkg/lock - open (11: Resource temporarily unavailable)
E: Unable to lock the administration directory (/var/lib/dpkg/), is another process using it?

Then when I go to Virtualmin web tool. This error shows:

Error - Perl execution failed

Can't locate lib.pm in @INC (you may need to install the lib module) (@INC contains: /usr/share/webmin /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl . /usr/share/webmin/ ..) at /usr/share/webmin/authentic-theme/index.cgi line 14.
BEGIN failed--compilation aborted at /usr/share/webmin/authentic-theme/index.cgi line 14.

Please help. All of my services are there.

Thanks, Anh

Status: 
Active

Comments

Howdy -- yeah unfortunately an interrupted upgrade process can cause some pretty serious problems.

Can you paste in the output of the command "ps auxwf"?

Also, how long ago did that outage occur?

Okay, it looks like there is a screen session that the upgrade process setup, which you may be able to re-connect to in order to continue the process.

There are details on how to do that in the link here:

http://serverfault.com/questions/387547/how-do-i-reattach-to-ubuntu-serv...

The accepted "Answer" to that question starts with running this command:

sudo screen -list

And then they show how to re-attach to that particular session.

Let us know if that allows you to continue the upgrade process.

Hi,

I was able to continue the upgrade process. Thank you so much. After finishing this show:

Welcome to Ubuntu 16.04.1 LTS (GNU/Linux 4.4.0-38-generic x86_64)

* Documentation:  https://help.ubuntu.com
* Management:     https://landscape.canonical.com
* Support:        https://ubuntu.com/advantage

  Get cloud support with Ubuntu Advantage Cloud Guest:
    http://www.ubuntu.com/business/services/cloud
New release '16.04.1 LTS' available.
Run 'do-release-upgrade' to upgrade to it.


*** System restart required ***
No mail.
Last login: Tue Oct 11 15:14:37 2016 from 115.73.29.184
root@JWeb:~# screen -d -r root/26798.ubuntu-release-upgrade-screen-window
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for dbus (1.10.6-1ubuntu3) ...
Processing triggers for dovecot-core (1:2.2.22-1ubuntu2.1) ...
dovecot stop/waiting
dovecot start/running, process 52727
Errors were encountered while processing:
mysql-server-5.7
mysql-server
Error in function:


*** Send problem report to the developers?

After the problem report has been sent, please fill out the form in the
automatically opened web browser.

What would you like to do? Your options are:
  S: Send report (475.8 KB)
  V: View report
  K: Keep report file for sending later or copying to somewhere else
  I: Cancel and ignore future crashes of this program version
  C: Cancel
Please choose (S/V/K/I/C):

And ind /etc/apt/sources.list I cannot find Virtualmin repositories. The webmin website still show: Error - Perl execution failed

Okay, let's review those issues one at a time there --

Regarding the first one, the error report -- that seems to indicate that the upgrade process isn't yet completed.

It's your choice there whether or not to send an error report -- though you might in this case just want to delay that for later by selecting "K" at that prompt.

That should continue the upgrade process, and allow you to send a report later if you wish.

Hi. Yes it was finished. Please help me on the rest. I cannot even run apache now.

We're happy to help! Note though that this is going to take some time.

Performing an upgrade is already a huge change, but when something like this occurs during the process it adds even more complexity.

So we're here to help, but I'd prepare for some extended downtime until it can all be resolved.

Let's take a look at the Apache issue next -- what problem do you experience when trying to start Apache?

If you look in the Apache error logs located in /var/log/apache2/error_log, you may see some log details there that would be helpful. What messages are in there?

root@JWeb:~# sudo systemctl start apache2
Job for apache2.service failed because the control process exited with error code. See "systemctl status apache2.service" and "journalctl -xe" for details.

And log:

[Sun Oct 09 06:40:46.262806 2016] [core:notice] [pid 2382] AH00094: Command line: '/usr/sbin/apache2'
[Sun Oct 09 06:40:52.335962 2016] [mpm_prefork:notice] [pid 2382] AH00171: Graceful restart requested, doing restart
AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 10.0.0.4. Set the 'ServerName' directive globally to suppress this message
[Sun Oct 09 06:40:52.412923 2016] [auth_digest:notice] [pid 2382] AH01757: generating secret for digest authentication ...
[Sun Oct 09 06:40:52.436512 2016] [ssl:warn] [pid 2382] AH02292: Init: Name-based SSL virtual hosts only work for clients with TLS server name indication support (RFC 4366)
[Sun Oct 09 06:40:52.436605 2016] [mpm_prefork:notice] [pid 2382] AH00163: Apache/2.4.7 (Ubuntu) SVN/1.8.8 mod_fcgid/2.3.9 PHP/5.5.9-1ubuntu4.20 OpenSSL/1.0.1f configured -- resuming normal operations
[Sun Oct 09 06:40:52.436613 2016] [core:notice] [pid 2382] AH00094: Command line: '/usr/sbin/apache2'
[Sun Oct 09 09:15:28.926212 2016] [mpm_prefork:error] [pid 2382] AH00161: server reached MaxRequestWorkers setting, consider raising the MaxRequestWorkers setting
[Mon Oct 10 02:36:17.832586 2016] [core:error] [pid 13480] [client 183.129.160.229:56024] AH00135: Invalid method in request test
[Tue Oct 11 12:49:43.157155 2016] [mpm_prefork:notice] [pid 2382] AH00169: caught SIGTERM, shutting down
[Tue Oct 11 12:49:44.211145 2016] [ssl:warn] [pid 17861] AH02292: Init: Name-based SSL virtual hosts only work for clients with TLS server name indication support (RFC 4366)
[Tue Oct 11 12:49:44.211155 2016] [suexec:notice] [pid 17861] AH01232: suEXEC mechanism enabled (wrapper: /usr/lib/apache2/suexec)
[Tue Oct 11 12:49:44.232383 2016] [auth_digest:notice] [pid 17862] AH01757: generating secret for digest authentication ...
[Tue Oct 11 12:49:44.252912 2016] [ssl:warn] [pid 17862] AH02292: Init: Name-based SSL virtual hosts only work for clients with TLS server name indication support (RFC 4366)
[Tue Oct 11 12:49:44.257053 2016] [mpm_prefork:notice] [pid 17862] AH00163: Apache/2.4.7 (Ubuntu) SVN/1.8.8 mod_fcgid/2.3.9 PHP/5.5.9-1ubuntu4.20 OpenSSL/1.0.1f configured -- resuming normal operations
[Tue Oct 11 12:49:44.257067 2016] [core:notice] [pid 17862] AH00094: Command line: '/usr/sbin/apache2'
[Tue Oct 11 14:59:46.337312 2016] [mpm_prefork:notice] [pid 17862] AH00169: caught SIGTERM, shutting down

Hmm, I don't see an obvious error there that would indicate why it's not starting.

What you may want to do, is run the two commands mentioned in the error output.

That is, after trying to start Apache, what is the output of these two commands:

systemctl status apache2.service
journalctl -xe

Here it is.

root@JWeb:~# systemctl status apache2.service
● apache2.service - LSB: Apache2 web server
   Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled)
  Drop-In: /lib/systemd/system/apache2.service.d
           └─apache2-systemd.conf
   Active: failed (Result: exit-code) since Tue 2016-10-11 21:44:47 UTC; 9s ago
     Docs: man:systemd-sysv-generator(8)
  Process: 12604 ExecStart=/etc/init.d/apache2 start (code=exited, status=1/FAIL

Oct 11 21:44:47 JWeb apache2[12604]: Output of config test was:
Oct 11 21:44:47 JWeb apache2[12604]: [Tue Oct 11 21:44:47.713237 2016] [so:warn]
Oct 11 21:44:47 JWeb apache2[12604]: AH00526: Syntax error on line 38 of /etc/ap
Oct 11 21:44:47 JWeb apache2[12604]: Invalid command 'php_admin_value', perhaps
Oct 11 21:44:47 JWeb apache2[12604]: Action 'configtest' failed.
Oct 11 21:44:47 JWeb apache2[12604]: The Apache error log may have more informat
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Control process exited, code=e
Oct 11 21:44:47 JWeb systemd[1]: Failed to start LSB: Apache2 web server.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Unit entered failed state.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Failed with result 'exit-code'
...skipping...
● apache2.service - LSB: Apache2 web server
   Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled)
  Drop-In: /lib/systemd/system/apache2.service.d
           └─apache2-systemd.conf
   Active: failed (Result: exit-code) since Tue 2016-10-11 21:44:47 UTC; 9s ago
     Docs: man:systemd-sysv-generator(8)
  Process: 12604 ExecStart=/etc/init.d/apache2 start (code=exited, status=1/FAIL

Oct 11 21:44:47 JWeb apache2[12604]: Output of config test was:
Oct 11 21:44:47 JWeb apache2[12604]: [Tue Oct 11 21:44:47.713237 2016] [so:warn]
Oct 11 21:44:47 JWeb apache2[12604]: AH00526: Syntax error on line 38 of /etc/ap
Oct 11 21:44:47 JWeb apache2[12604]: Invalid command 'php_admin_value', perhaps
Oct 11 21:44:47 JWeb apache2[12604]: Action 'configtest' failed.
Oct 11 21:44:47 JWeb apache2[12604]: The Apache error log may have more informat
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Control process exited, code=e
Oct 11 21:44:47 JWeb systemd[1]: Failed to start LSB: Apache2 web server.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Unit entered failed state.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Failed with result 'exit-code'
~
~
~
~
~
ESCOC
ver
bad; vendor preset: enabled)
ervice.d

nce Tue 2016-10-11 21:44:47 UTC; 9s ago

pache2 start (code=exited, status=1/FAILURE)

put of config test was:
e Oct 11 21:44:47.713237 2016] [so:warn] [pid 12614] AH01574: module dav_module
0526: Syntax error on line 38 of /etc/apache2/sites-enabled/adanhgia.com.conf:
alid command 'php_admin_value', perhaps misspelled or defined by a module not in
ion 'configtest' failed.
Apache error log may have more information.
.service: Control process exited, code=exited status=1
to start LSB: Apache2 web server.
.service: Unit entered failed state.
.service: Failed with result 'exit-code'.
~
~
~
~
~
ESCOD
● apache2.service - LSB: Apache2 web server
   Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled)
  Drop-In: /lib/systemd/system/apache2.service.d
           └─apache2-systemd.conf
   Active: failed (Result: exit-code) since Tue 2016-10-11 21:44:47 UTC; 9s ago
     Docs: man:systemd-sysv-generator(8)
  Process: 12604 ExecStart=/etc/init.d/apache2 start (code=exited, status=1/FAIL

Oct 11 21:44:47 JWeb apache2[12604]: Output of config test was:
Oct 11 21:44:47 JWeb apache2[12604]: [Tue Oct 11 21:44:47.713237 2016] [so:warn]
Oct 11 21:44:47 JWeb apache2[12604]: AH00526: Syntax error on line 38 of /etc/ap
Oct 11 21:44:47 JWeb apache2[12604]: Invalid command 'php_admin_value', perhaps
Oct 11 21:44:47 JWeb apache2[12604]: Action 'configtest' failed.
Oct 11 21:44:47 JWeb apache2[12604]: The Apache error log may have more informat
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Control process exited, code=e
Oct 11 21:44:47 JWeb systemd[1]: Failed to start LSB: Apache2 web server.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Unit entered failed state.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Failed with result 'exit-code'
~
~
~
~
~
ESCOD
● apache2.service - LSB: Apache2 web server
   Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled)
  Drop-In: /lib/systemd/system/apache2.service.d
           └─apache2-systemd.conf
   Active: failed (Result: exit-code) since Tue 2016-10-11 21:44:47 UTC; 9s ago
     Docs: man:systemd-sysv-generator(8)
  Process: 12604 ExecStart=/etc/init.d/apache2 start (code=exited, status=1/FAIL

Oct 11 21:44:47 JWeb apache2[12604]: Output of config test was:
Oct 11 21:44:47 JWeb apache2[12604]: [Tue Oct 11 21:44:47.713237 2016] [so:warn]
Oct 11 21:44:47 JWeb apache2[12604]: AH00526: Syntax error on line 38 of /etc/ap
Oct 11 21:44:47 JWeb apache2[12604]: Invalid command 'php_admin_value', perhaps
Oct 11 21:44:47 JWeb apache2[12604]: Action 'configtest' failed.
Oct 11 21:44:47 JWeb apache2[12604]: The Apache error log may have more informat
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Control process exited, code=e
Oct 11 21:44:47 JWeb systemd[1]: Failed to start LSB: Apache2 web server.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Unit entered failed state.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Failed with result 'exit-code'
~
~
~
~
~
ESCOD
● apache2.service - LSB: Apache2 web server
   Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled)
  Drop-In: /lib/systemd/system/apache2.service.d
           └─apache2-systemd.conf
   Active: failed (Result: exit-code) since Tue 2016-10-11 21:44:47 UTC; 9s ago
     Docs: man:systemd-sysv-generator(8)
  Process: 12604 ExecStart=/etc/init.d/apache2 start (code=exited, status=1/FAIL

Oct 11 21:44:47 JWeb apache2[12604]: Output of config test was:
Oct 11 21:44:47 JWeb apache2[12604]: [Tue Oct 11 21:44:47.713237 2016] [so:warn]
Oct 11 21:44:47 JWeb apache2[12604]: AH00526: Syntax error on line 38 of /etc/ap
Oct 11 21:44:47 JWeb apache2[12604]: Invalid command 'php_admin_value', perhaps
Oct 11 21:44:47 JWeb apache2[12604]: Action 'configtest' failed.
Oct 11 21:44:47 JWeb apache2[12604]: The Apache error log may have more informat
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Control process exited, code=e
Oct 11 21:44:47 JWeb systemd[1]: Failed to start LSB: Apache2 web server.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Unit entered failed state.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Failed with result 'exit-code'
~
~
~
~
~

root@JWeb:~# journalctl -xe
Oct 11 21:44:47 JWeb apache2[12604]: Action 'configtest' failed.
Oct 11 21:44:47 JWeb apache2[12604]: The Apache error log may have more informat
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Control process exited, code=e
Oct 11 21:44:47 JWeb systemd[1]: Failed to start LSB: Apache2 web server.
-- Subject: Unit apache2.service has failed
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit apache2.service has failed.
--
-- The result is failed.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Unit entered failed state.
Oct 11 21:44:47 JWeb systemd[1]: apache2.service: Failed with result 'exit-code'
Oct 11 21:44:47 JWeb sudo[12600]: pam_unix(sudo:session): session closed for use
Oct 11 21:44:48 JWeb sshd[12595]: Failed password for root from 112.85.218.11 po
Oct 11 21:44:48 JWeb sshd[12595]: Received disconnect from 112.85.218.11 port 48
Oct 11 21:44:48 JWeb sshd[12595]: Disconnected from 112.85.218.11 port 48100 [pr
Oct 11 21:44:48 JWeb sshd[12595]: PAM 2 more authentication failures; logname= u
Oct 11 21:45:01 JWeb CRON[12631]: pam_unix(cron:session): session opened for use
Oct 11 21:45:01 JWeb CRON[12633]: (root) CMD (command -v debian-sa1 > /dev/null
Oct 11 21:45:01 JWeb CRON[12632]: pam_unix(cron:session): session opened for use
Oct 11 21:45:01 JWeb CRON[12635]: (root) CMD (/etc/webmin/status/monitor.pl)
Oct 11 21:45:01 JWeb CRON[12631]: pam_unix(cron:session): session closed for use
lines 2813-2835/2835 (END)

Ah there we go, the error in question is this one here:

Oct 11 21:44:47 JWeb apache2[12604]: Invalid command 'php_admin_value', perhaps
Oct 11 21:44:47 JWeb apache2[12604]: Action 'configtest' failed.

That suggests that mod_php isn't loading (or installed).

While you can always disable all the lines in the Apache config that begin with "php_admin_value", we can also get mod_php loaded.

What is the output of these two commands:

dpkg -l 'libapache2-mod-php*'
ls /etc/apache2/mods-enabled

Hi,

root@JWeb:~# dpkg -l 'libapache2-mod-php*'
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name           Version      Architecture Description
+++-==============-============-============-=================================
un  libapache2-mod <none>       <none>       (no description available)
un  libapache2-mod <none>       <none>       (no description available)
root@JWeb:~# ls /etc/apache2/mods-enabled
access_compat.load  autoindex.conf  fcgid.load           proxy.load
actions.conf        autoindex.load  filter.load          rewrite.load
actions.load        dav_fs.conf     mime.conf            setenvif.conf
alias.conf          dav_fs.load     mime.load            setenvif.load
alias.load          dav.load        mpm_prefork.conf     slotmem_shm.load
auth_basic.load     dav_svn.conf    mpm_prefork.load     socache_shmcb.load
auth_digest.load    dav_svn.load    negotiation.conf     ssl.conf
authn_core.load     deflate.conf    negotiation.load     ssl.load
authn_file.load     deflate.load    proxy_balancer.conf  status.conf
authz_core.load     dir.conf        proxy_balancer.load  status.load
authz_host.load     dir.load        proxy.conf           suexec.load
authz_svn.load      env.load        proxy_connect.load
authz_user.load     fcgid.conf      proxy_http.load

Okay, it doesn't look like that's installed. Try running this command:

apt-get install libapache2-mod-php

After running that command, try to start Apache. Is it able to load at that point?

I was able to start apache2. But mysql was not:

root@JWeb:~# apt-get install libapache2-mod-php
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
  gcc-4.8 libboost-iostreams1.58.0 libisl10 libmcrypt4 libmemcached10
  libterm-readkey-perl libvpx1 linux-headers-3.16.0-45
  linux-headers-3.16.0-45-generic linux-headers-3.16.0-46
  linux-headers-3.16.0-46-generic linux-headers-3.16.0-48
  linux-headers-3.16.0-48-generic linux-headers-3.16.0-50
  linux-headers-3.16.0-50-generic linux-headers-3.16.0-51
  linux-headers-3.16.0-51-generic linux-headers-3.16.0-53
  linux-headers-3.16.0-53-generic linux-headers-3.16.0-56
  linux-headers-3.16.0-56-generic linux-headers-3.16.0-57
  linux-headers-3.16.0-57-generic linux-headers-3.16.0-59
  linux-headers-3.16.0-59-generic linux-headers-3.16.0-60
  linux-headers-3.16.0-60-generic linux-headers-3.16.0-62
  linux-headers-3.16.0-62-generic linux-headers-3.16.0-67
  linux-headers-3.16.0-67-generic linux-headers-3.16.0-70
  linux-headers-3.16.0-70-generic linux-headers-3.16.0-71
  linux-headers-3.16.0-71-generic linux-headers-3.16.0-73
  linux-headers-3.16.0-73-generic linux-headers-3.16.0-77
  linux-headers-3.16.0-77-generic linux-headers-virtual-lts-xenial
  linux-image-3.16.0-45-generic linux-image-3.16.0-46-generic
  linux-image-3.16.0-48-generic linux-image-3.16.0-50-generic
  linux-image-3.16.0-51-generic linux-image-3.16.0-53-generic
  linux-image-3.16.0-56-generic linux-image-3.16.0-57-generic
  linux-image-3.16.0-59-generic linux-image-3.16.0-60-generic
  linux-image-3.16.0-62-generic linux-image-3.16.0-67-generic
  linux-image-3.16.0-70-generic linux-image-3.16.0-71-generic
  linux-image-3.16.0-73-generic linux-image-3.16.0-77-generic
  linux-image-3.19.0-25-generic linux-image-3.19.0-26-generic
  linux-image-3.19.0-30-generic linux-image-3.19.0-31-generic
  linux-image-3.19.0-33-generic linux-image-3.19.0-41-generic
  linux-image-3.19.0-42-generic linux-image-3.19.0-43-generic
  linux-image-3.19.0-47-generic linux-image-3.19.0-49-generic
  linux-image-3.19.0-51-generic linux-image-3.19.0-56-generic
  linux-image-3.19.0-58-generic linux-image-3.19.0-59-generic
  linux-image-3.19.0-61-generic linux-image-3.19.0-65-generic
  linux-image-3.19.0-66-generic linux-image-3.19.0-69-generic
  linux-image-3.19.0-71-generic
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  libapache2-mod-php7.0
The following NEW packages will be installed:
  libapache2-mod-php libapache2-mod-php7.0
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
2 not fully installed or removed.
Need to get 1,227 kB of archives.
After this operation, 4,323 kB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://azure.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libapache2-mod-php7.0 amd64 7.0.8-0ubuntu0.16.04.3 [1,224 kB]
Get:2 http://azure.archive.ubuntu.com/ubuntu xenial/main amd64 libapache2-mod-php all 1:7.0+35ubuntu6 [2,960 B]
Fetched 1,227 kB in 0s (3,017 kB/s)
Selecting previously unselected package libapache2-mod-php7.0.
(Reading database ... 606874 files and directories currently installed.)
Preparing to unpack .../libapache2-mod-php7.0_7.0.8-0ubuntu0.16.04.3_amd64.deb ...
Unpacking libapache2-mod-php7.0 (7.0.8-0ubuntu0.16.04.3) ...
Selecting previously unselected package libapache2-mod-php.
Preparing to unpack .../libapache2-mod-php_1%3a7.0+35ubuntu6_all.deb ...
Unpacking libapache2-mod-php (1:7.0+35ubuntu6) ...
Setting up mysql-server-5.7 (5.7.15-0ubuntu0.16.04.1) ...
Renaming removed key_buffer and myisam-recover options (if present)
ERROR: Unable to start MySQL server:
2016-10-12T01:03:05.609800Z 0 [ERROR] unknown variable 'thread_concurrency=8'
2016-10-12T01:03:05.612459Z 0 [ERROR] Aborting
Please take a look at https://wiki.debian.org/Teams/MySQL/FAQ for tips on fixing common upgrade issues.
Once the problem is resolved, run apt-get --fix-broken install to retry.
dpkg: error processing package mysql-server-5.7 (--configure):
subprocess installed post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of mysql-server:
mysql-server depends on mysql-server-5.7; however:
  Package mysql-server-5.7 is not configured yet.

dpkg: error processing package mysql-server (--configure):
dependency problems - leaving unconfigured
Setting up libapache2-mod-php7.0 (7.0.8-0ubuntu0.16.04.3) ...
No apport report written because the error message indicates its a followup error from a previous failure.

Creating config file /etc/php/7.0/apache2/php.ini with new version
apache2_invoke: Enable module php7.0
Setting up libapache2-mod-php (1:7.0+35ubuntu6) ...
Errors were encountered while processing:
mysql-server-5.7
mysql-server
E: Sub-process /usr/bin/dpkg returned an error code (1)
root@JWeb:~# systemctl status mysql.service
● mysql.service - MySQL Community Server
   Loaded: loaded (/lib/systemd/system/mysql.service; disabled; vendor preset: e
   Active: activating (start-post) (Result: exit-code) since Wed 2016-10-12 01:0
  Process: 4340 ExecStart=/usr/sbin/mysqld (code=exited, status=1/FAILURE)
  Process: 4337 ExecStartPre=/usr/share/mysql/mysql-systemd-start pre (code=exit
Main PID: 4340 (code=exited, status=1/FAILURE);         : 4341 (mysql-systemd-s
    Tasks: 2
   Memory: 324.0K
      CPU: 308ms
   CGroup: /system.slice/mysql.service
           └─control
             ├─4341 /bin/bash /usr/share/mysql/mysql-systemd-start post
             └─4396 sleep 1

Oct 12 01:07:26 JWeb systemd[1]: mysql.service: Service hold-off time over, sche
Oct 12 01:07:26 JWeb systemd[1]: Stopped MySQL Community Server.
Oct 12 01:07:26 JWeb systemd[1]: Starting MySQL Community Server...
Oct 12 01:07:28 JWeb systemd[1]: mysql.service: Main process exited, code=exited
lines 1-18/18 (END)
root@JWeb:~# journalctl -xe                                                     Oct 12 01:08:56 JWeb systemd[1]: mysql.service: Unit entered failed state.
Oct 12 01:08:56 JWeb systemd[1]: mysql.service: Failed with result 'exit-code'.
Oct 12 01:08:57 JWeb sshd[4776]: Failed password for root from 221.194.47.208 po
Oct 12 01:08:57 JWeb sshd[4776]: Received disconnect from 221.194.47.208 port 53
Oct 12 01:08:57 JWeb sshd[4776]: Disconnected from 221.194.47.208 port 53003 [pr
Oct 12 01:08:57 JWeb sshd[4776]: PAM 2 more authentication failures; logname= ui
Oct 12 01:08:57 JWeb systemd[1]: mysql.service: Service hold-off time over, sche
Oct 12 01:08:57 JWeb systemd[1]: Stopped MySQL Community Server.
-- Subject: Unit mysql.service has finished shutting down
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit mysql.service has finished shutting down.
Oct 12 01:08:57 JWeb systemd[1]: Starting MySQL Community Server...
-- Subject: Unit mysql.service has begun start-up
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit mysql.service has begun starting up.
Oct 12 01:08:57 JWeb audit[4799]: AVC apparmor="DENIED" operation="open" profile
Oct 12 01:08:57 JWeb kernel: audit: type=1400 audit(1476234537.122:372): apparmo
Oct 12 01:08:57 JWeb sshd[4804]: pam_unix(sshd:auth): authentication failure; lo
Oct 12 01:08:59 JWeb systemd[1]: mysql.service: Main process exited, code=exited

It looks like there is a MySQL issue at the moment that is preventing things from being installed. It also prevented the MySQL upgrade from completing.

It appears to be a simple fix though -- if you look in /etc/my.cnf, do you see a line beginning with the word "thread_concurrency"?

If so, comment out or delete that, and then run this command:

dpkg --configure -a

The above command should be able to complete successfully... or if it doesn't, let us know what the output is.

Hi,

Here is the content of that file. I guess it's not the correct one?

[mysqld]
open_files_limit = 100000

And here is the result:

root@JWeb:~# dpkg --configure -a
Setting up mysql-server-5.7 (5.7.15-0ubuntu0.16.04.1) ...
Renaming removed key_buffer and myisam-recover options (if present)
ERROR: Unable to start MySQL server:
2016-10-12T03:10:28.879324Z 0 [ERROR] unknown variable 'thread_concurrency=8'
2016-10-12T03:10:28.882244Z 0 [ERROR] Aborting
Please take a look at https://wiki.debian.org/Teams/MySQL/FAQ for tips on fixing common upgrade issues.
Once the problem is resolved, run apt-get --fix-broken install to retry.
dpkg: error processing package mysql-server-5.7 (--configure):
subprocess installed post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of mysql-server:
mysql-server depends on mysql-server-5.7; however:
  Package mysql-server-5.7 is not configured yet.

dpkg: error processing package mysql-server (--configure):
dependency problems - leaving unconfigured
Errors were encountered while processing:
mysql-server-5.7
mysql-server

Hrm, well that's certainly odd, I was definitely expecting to see more lines there.

How about this -- we can do a search through the entire /etc directory:

find /etc | xargs grep thread_concurrency

What is the output of that command?

Here it is:

root@JWeb:~# find /etc | xargs grep thread_concurrency
grep: /etc: Is a directory
grep: /etc/lvm: Is a directory
grep: /etc/ldap: Is a directory
grep: /etc/landscape: Is a directory
grep: /etc/samba: Is a directory
grep: /etc/samba/tls: Is a directory
grep: /etc/mailman: Is a directory
grep: /etc/mailman/en: Is a directory
grep: /etc/mailman/vi: Is a directory
grep: /etc/xdg: Is a directory
grep: /etc/xdg/autostart: Is a directory
grep: /etc/xdg/systemd: Is a directory
grep: /etc/xdg/systemd/user: Is a directory
grep: /etc/xml: Is a directory
grep: /etc/terminfo: Is a directory
grep: /etc/cron.hourly: Is a directory
grep: /etc/webalizer: Is a directory
grep: /etc/init.d: Is a directory
grep: /etc/X11: Is a directory
grep: /etc/X11/xkb: Is a directory
grep: /etc/X11/xinit: Is a directory
grep: /etc/X11/xinit/xinitrc.d: Is a directory
grep: /etc/X11/Xsession.d: Is a directory
grep: /etc/init: Is a directory
grep: /etc/dbus-1: Is a directory
grep: /etc/dbus-1/session.d: Is a directory
grep: /etc/dbus-1/system.d: Is a directory
grep: /etc/cloud: Is a directory
grep: /etc/cloud/cloud.cfg.d: Is a directory
grep: /etc/cloud/templates: Is a directory
grep: /etc/thermald: Is a directory
grep: /etc/apache2: Is a directory
grep: /etc/apache2/mods-enabled: Is a directory
grep: /etc/apache2/mods-available: Is a directory
grep: /etc/apache2/conf-enabled: Is a directory
grep: /etc/apache2/conf-available: Is a directory
grep: /etc/apache2/sites-enabled: Is a directory
grep: /etc/apache2/suexec: Is a directory
grep: /etc/apache2/sites-available: Is a directory
grep: /etc/proftpd: Is a directory
grep: /etc/proftpd/conf.d: Is a directory
grep: /etc/skel: Is a directory
grep: /etc/calendar: Is a directory
grep: /etc/opt: Is a directory
grep: /etc/opt/microsoft: Is a directory
grep: /etc/opt/microsoft/mysql-cimprov: Is a directory
grep: /etc/opt/microsoft/mysql-cimprov/conf: Is a directory
grep: /etc/opt/microsoft/scx: Is a directory
grep: /etc/opt/microsoft/scx/ssl: Is a directory
grep: /etc/opt/microsoft/scx/conf: Is a directory
grep: /etc/opt/microsoft/scx/conf/sudodir: Is a directory
grep: /etc/opt/microsoft/scx/conf/.baseconf: Is a directory
grep: /etc/opt/microsoft/apache-cimprov: Is a directory
grep: /etc/opt/microsoft/apache-cimprov/conf: Is a directory
grep: /etc/opt/omi: Is a directory
grep: /etc/opt/omi/ssl: Is a directory
grep: /etc/opt/omi/conf: Is a directory
grep: /etc/opt/omi/conf/omiregister: Is a directory
grep: /etc/opt/omi/conf/omiregister/root-apache: Is a directory
grep: /etc/opt/omi/conf/omiregister/root-scx: Is a directory
grep: /etc/opt/omi/conf/omiregister/root-omi: Is a directory
grep: /etc/opt/omi/conf/omiregister/root-mysql: Is a directory
grep: /etc/ssl: Is a directory
grep: /etc/ssl/private: Is a directory
grep: /etc/ssl/certs: Is a directory
grep: /etc/rc5.d: Is a directory
grep: /etc/postgresql: Is a directory
grep: /etc/postgresql/9.3: Is a directory
grep: /etc/postgresql/9.3/main: Is a directory
grep: /etc/postgresql/9.5: Is a directory
grep: /etc/postgresql/9.5/main: Is a directory
grep: /etc/python3.5: Is a directory
grep: /etc/logcheck: Is a directory
grep: /etc/logcheck/ignore.d.server: Is a directory
grep: /etc/logcheck/ignore.d.paranoid: Is a directory
grep: /etc/logcheck/violations.d: Is a directory
grep: /etc/logcheck/ignore.d.workstation: Is a directory
grep: /etc/cron.monthly: Is a directory
grep: /etc/newt: Is a directory
grep: /etc/byobu: Is a directory
grep: /etc/mdadm: Is a directory
grep: /etc/pm: Is a directory
grep: /etc/pm/sleep.d: Is a directory
grep: /etc/grub.d: Is a directory
grep: /etc/iproute2: Is a directory
grep: /etc/acpi: Is a directory
grep: /etc/acpi/events: Is a directory
grep: /etc/insserv: Is a directory
grep: /etc/insserv/overrides: Is a directory
grep: /etc/php: Is a directory
grep: /etc/php/7.0: Is a directory
grep: /etc/php/7.0/apache2: Is a directory
grep: /etc/php/7.0/apache2/conf.d: Is a directory
grep: /etc/php/7.0/mods-available: Is a directory
grep: /etc/php/7.0/cli: Is a directory
grep: /etc/php/7.0/cli/conf.d: Is a directory
grep: /etc/kernel: Is a directory
grep: /etc/kernel/postinst.d: Is a directory
grep: /etc/kernel/kernel: Is a directory
grep: /etc/kernel/kernel/postinst.d: Is a directory
grep: /etc/kernel/kernel/postrm.d: Is a directory
grep: /etc/kernel/postrm.d: Is a directory
grep: /etc/scponly: Is a directory
grep: /etc/postfix: Is a directory
grep: /etc/postfix/sasl: Is a directory
grep: /etc/cron.weekly: Is a directory
grep: /etc/rc2.d: Is a directory
grep: /etc/update-manager: Is a directory
grep: /etc/update-manager/release-upgrades.d: Is a directory
grep: /etc/python2.7: Is a directory
grep: /etc/resolvconf: Is a directory
grep: /etc/resolvconf/update-libc.d: Is a directory
grep: /etc/resolvconf/update.d: Is a directory
grep: /etc/resolvconf/resolv.conf.d: Is a directory
grep: /etc/resolvconf/resolv.conf.d/tail: No such file or directory
grep: /etc/default: Is a directory
grep: /etc/default/grub.d: Is a directory
grep: /etc/selinux: Is a directory
grep: /etc/profile.d: Is a directory
grep: /etc/ld.so.conf.d: Is a directory
grep: /etc/rc6.d: Is a directory
grep: /etc/cron.daily: Is a directory
grep: /etc/groff: Is a directory
grep: /etc/alternatives: Is a directory
/etc/alternatives/my.cnf:thread_concurrency = 8
grep: /etc/sensors.d: Is a directory
grep: /etc/rc3.d: Is a directory
grep: /etc/apport: Is a directory
grep: /etc/apport/blacklist.d: Is a directory
grep: /etc/update-motd.d: Is a directory
grep: /etc/vmware-tools: Is a directory
grep: /etc/vmware-tools/scripts: Is a directory
grep: /etc/vmware-tools/scripts/vmware: Is a directory
grep: /etc/ca-certificates: Is a directory
grep: /etc/ca-certificates/update.d: Is a directory
grep: /etc/ufw: Is a directory
grep: /etc/ufw/applications.d: Is a directory
grep: /etc/ufw/applications.d/apache2: Is a directory
grep: /etc/python3.4: Is a directory
grep: /etc/ppp: Is a directory
grep: /etc/ppp/ip-down.d: Is a directory
grep: /etc/ppp/peers: Is a directory
grep: /etc/ppp/resolv: Is a directory
grep: /etc/ppp/ip-up.d: Is a directory
grep: /etc/ppp/ipv6-up.d: Is a directory
grep: /etc/ppp/ipv6-down.d: Is a directory
grep: /etc/dovecot: Is a directory
grep: /etc/dovecot/private: Is a directory
grep: /etc/dovecot/conf.d: Is a directory
grep: /etc/mysql: Is a directory
grep: /etc/mysql/mysql.conf.d: Is a directory
/etc/mysql/mysql.conf.d/mysqld.cnf:#thread_concurrency     = 10
/etc/mysql/my.cnf:thread_concurrency = 8
/etc/mysql/my.cnf.migrated:thread_concurrency = 8
grep: /etc/mysql/conf.d: Is a directory
grep: /etc/modules-load.d: Is a directory
grep: /etc/request-key.d: Is a directory
grep: /etc/kbd: Is a directory
grep: /etc/python: Is a directory
grep: /etc/binfmt.d: Is a directory
grep: /etc/pollinate: Is a directory
grep: /etc/rc1.d: Is a directory
grep: /etc/bash_completion.d: Is a directory
grep: /etc/rcS.d: Is a directory
grep: /etc/chatscripts: Is a directory
grep: /etc/vim: Is a directory
grep: /etc/cron.d: Is a directory
grep: /etc/php5: Is a directory
grep: /etc/php5/mods-available: Is a directory
grep: /etc/php5/cli: Is a directory
grep: /etc/php5/cgi: Is a directory
grep: /etc/modprobe.d: Is a directory
grep: /etc/rsyslog.d: Is a directory
grep: /etc/initramfs-tools: Is a directory
grep: /etc/initramfs-tools/scripts: Is a directory
grep: /etc/initramfs-tools/scripts/local-premount: Is a directory
grep: /etc/initramfs-tools/scripts/nfs-bottom: Is a directory
grep: /etc/initramfs-tools/scripts/nfs-top: Is a directory
grep: /etc/initramfs-tools/scripts/init-top: Is a directory
grep: /etc/initramfs-tools/scripts/local-bottom: Is a directory
grep: /etc/initramfs-tools/scripts/nfs-premount: Is a directory
grep: /etc/initramfs-tools/scripts/panic: Is a directory
grep: /etc/initramfs-tools/scripts/local-top: Is a directory
grep: /etc/initramfs-tools/scripts/init-bottom: Is a directory
grep: /etc/initramfs-tools/scripts/init-premount: Is a directory
grep: /etc/initramfs-tools/conf.d: Is a directory
grep: /etc/initramfs-tools/hooks: Is a directory
grep: /etc/iscsi: Is a directory
grep: /etc/pear: Is a directory
grep: /etc/sysctl.d: Is a directory
grep: /etc/insserv.conf.d: Is a directory
grep: /etc/gss: Is a directory
grep: /etc/gss/mech.d: Is a directory
grep: /etc/security: Is a directory
grep: /etc/security/limits.d: Is a directory
grep: /etc/security/namespace.d: Is a directory
grep: /etc/fonts: Is a directory
grep: /etc/fonts/conf.d: Is a directory
grep: /etc/fonts/conf.avail: Is a directory
grep: /etc/dpkg: Is a directory
grep: /etc/dpkg/origins: Is a directory
grep: /etc/dpkg/dpkg.cfg.d: Is a directory
grep: /etc/bind: Is a directory
grep: /etc/subversion: Is a directory
grep: /etc/update-notifier: Is a directory
grep: /etc/python3: Is a directory
grep: /etc/console-setup: Is a directory
grep: /etc/apparmor.d: Is a directory
grep: /etc/apparmor.d/disable: Is a directory
grep: /etc/apparmor.d/abstractions: Is a directory
grep: /etc/apparmor.d/abstractions/ubuntu-browsers.d: Is a directory
grep: /etc/apparmor.d/abstractions/lxc: Is a directory
grep: /etc/apparmor.d/abstractions/apparmor_api: Is a directory
grep: /etc/apparmor.d/tunables: Is a directory
grep: /etc/apparmor.d/tunables/home.d: Is a directory
grep: /etc/apparmor.d/tunables/xdg-user-dirs.d: Is a directory
grep: /etc/apparmor.d/tunables/multiarch.d: Is a directory
grep: /etc/apparmor.d/lxc: Is a directory
grep: /etc/apparmor.d/local: Is a directory
grep: /etc/apparmor.d/cache: Is a directory
grep: /etc/apparmor.d/force-complain: Is a directory
grep: /etc/perl: Is a directory
grep: /etc/perl/Net: Is a directory
grep: /etc/perl/XML: Is a directory
grep: /etc/perl/XML/SAX: Is a directory
grep: /etc/perl/CPAN: Is a directory
grep: /etc/dhcp: Is a directory
grep: /etc/dhcp/dhclient-enter-hooks.d: Is a directory
grep: /etc/dhcp/dhclient-exit-hooks.d: Is a directory
grep: /etc/systemd: Is a directory
grep: /etc/systemd/user: Is a directory
grep: /etc/systemd/system: Is a directory
grep: /etc/systemd/system/shutdown.target.wants: Is a directory
grep: /etc/systemd/system/sysinit.target.wants: Is a directory
grep: /etc/systemd/system/paths.target.wants: Is a directory
grep: /etc/systemd/system/sockets.target.wants: Is a directory
grep: /etc/systemd/system/clamav-daemon.socket.d: Is a directory
grep: /etc/systemd/system/getty.target.wants: Is a directory
grep: /etc/systemd/system/multi-user.target.wants: Is a directory
grep: /etc/systemd/system/graphical.target.wants: Is a directory
grep: /etc/systemd/system/default.target.wants: Is a directory
grep: /etc/systemd/system/cloud-init.target.wants: Is a directory
grep: /etc/systemd/system/timers.target.wants: Is a directory
grep: /etc/systemd/system/network-online.target.wants: Is a directory
grep: /etc/systemd/network: Is a directory
grep: /etc/awstats: Is a directory
grep: /etc/apm: Is a directory
grep: /etc/apm/event.d: Is a directory
grep: /etc/sudoers.d: Is a directory
grep: /etc/NetworkManager: Is a directory
grep: /etc/NetworkManager/dispatcher.d: Is a directory
grep: /etc/depmod.d: Is a directory
grep: /etc/polkit-1: Is a directory
grep: /etc/polkit-1/localauthority.conf.d: Is a directory
grep: /etc/polkit-1/localauthority: Is a directory
grep: /etc/polkit-1/localauthority/90-mandatory.d: Is a directory
grep: /etc/polkit-1/localauthority/30-site.d: Is a directory
grep: /etc/polkit-1/localauthority/20-org.d: Is a directory
grep: /etc/polkit-1/localauthority/10-vendor.d: Is a directory
grep: /etc/polkit-1/localauthority/50-local.d: Is a directory
grep: /etc/polkit-1/nullbackend.conf.d: Is a directory
grep: /etc/lighttpd: Is a directory
grep: /etc/lighttpd/conf-enabled: Is a directory
grep: /etc/lighttpd/conf-available: Is a directory
grep: /etc/spamassassin: Is a directory
grep: /etc/spamassassin/sa-update-hooks.d: Is a directory
grep: /etc/spamassassin/sa-update-keys: Is a directory
grep: /etc/webmin: Is a directory
grep: /etc/webmin/iscsi-tgtd: Is a directory
grep: /etc/webmin/lvm: Is a directory
grep: /etc/webmin/webmincron: Is a directory
grep: /etc/webmin/webmincron/crons: Is a directory
grep: /etc/webmin/backup-config: Is a directory
grep: /etc/webmin/sshd: Is a directory
grep: /etc/webmin/cluster-useradmin: Is a directory
grep: /etc/webmin/vgetty: Is a directory
grep: /etc/webmin/samba: Is a directory
grep: /etc/webmin/security-updates: Is a directory
grep: /etc/webmin/status: Is a directory
grep: /etc/webmin/status/services: Is a directory
grep: /etc/webmin/status/history: Is a directory
grep: /etc/webmin/cluster-copy: Is a directory
grep: /etc/webmin/heartbeat: Is a directory
grep: /etc/webmin/phpini: Is a directory
grep: /etc/webmin/cluster-passwd: Is a directory
grep: /etc/webmin/net: Is a directory
grep: /etc/webmin/servers: Is a directory
grep: /etc/webmin/sendmail: Is a directory
grep: /etc/webmin/webalizer: Is a directory
grep: /etc/webmin/package-updates: Is a directory
grep: /etc/webmin/init: Is a directory
grep: /etc/webmin/virtual-server: Is a directory
grep: /etc/webmin/virtual-server/links-cache: Is a directory
grep: /etc/webmin/virtual-server/template-scripts: Is a directory
grep: /etc/webmin/virtual-server/backups: Is a directory
grep: /etc/webmin/virtual-server/names: Is a directory
grep: /etc/webmin/virtual-server/everyone: Is a directory
grep: /etc/webmin/virtual-server/history: Is a directory
grep: /etc/webmin/virtual-server/scriptlog: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/14405233875182: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/145561016644494: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/14581039929263: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/14543470196477: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/144072525613121: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/145485940119040: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/14579243622306: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/144100547942763: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/146057346531996: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/14511053187760: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/144120875035160: Is a directory
grep: /etc/webmin/virtual-server/scriptlog/146062102117452: Is a directory
grep: /etc/webmin/virtual-server/spam: Is a directory
grep: /etc/webmin/virtual-server/spam/14405233875182: Is a directory
grep: /etc/webmin/virtual-server/spam/14405233875182/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/14405233875182/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/145561016644494: Is a directory
grep: /etc/webmin/virtual-server/spam/145561016644494/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/145561016644494/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/14581039929263: Is a directory
grep: /etc/webmin/virtual-server/spam/14581039929263/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/14581039929263/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/14543470196477: Is a directory
grep: /etc/webmin/virtual-server/spam/14543470196477/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/14543470196477/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/144120869134447: Is a directory
grep: /etc/webmin/virtual-server/spam/144120869134447/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/144120869134447/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/144099439133062: Is a directory
grep: /etc/webmin/virtual-server/spam/144099439133062/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/144099439133062/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/144120879535795: Is a directory
grep: /etc/webmin/virtual-server/spam/144120879535795/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/144120879535795/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/144072525613121: Is a directory
grep: /etc/webmin/virtual-server/spam/144072525613121/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/144072525613121/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/144101384248922: Is a directory
grep: /etc/webmin/virtual-server/spam/144101384248922/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/144101384248922/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/145485940119040: Is a directory
grep: /etc/webmin/virtual-server/spam/145485940119040/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/145485940119040/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/14579243622306: Is a directory
grep: /etc/webmin/virtual-server/spam/14579243622306/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/14579243622306/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/144100547942763: Is a directory
grep: /etc/webmin/virtual-server/spam/144100547942763/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/144100547942763/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/146057346531996: Is a directory
grep: /etc/webmin/virtual-server/spam/146057346531996/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/146057346531996/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/14511053187760: Is a directory
grep: /etc/webmin/virtual-server/spam/14511053187760/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/14511053187760/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/144120875035160: Is a directory
grep: /etc/webmin/virtual-server/spam/144120875035160/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/144120875035160/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/spam/146062102117452: Is a directory
grep: /etc/webmin/virtual-server/spam/146062102117452/sa-update-hooks.d: Is a directory
grep: /etc/webmin/virtual-server/spam/146062102117452/sa-update-keys: Is a directory
grep: /etc/webmin/virtual-server/hashpass: Is a directory
grep: /etc/webmin/virtual-server/nospam: Is a directory
grep: /etc/webmin/virtual-server/domains: Is a directory
grep: /etc/webmin/virtual-server/templates: Is a directory
grep: /etc/webmin/virtual-server/procmail: Is a directory
grep: /etc/webmin/virtual-server/plainpass: Is a directory
grep: unrecognized option '--id'
Usage: grep [OPTION]... PATTERN [FILE]...
Try 'grep --help' for more information.

Hmm, that search doesn't seem to have worked.

Is there a directory named "/etc/my.cnf.d/"? If so, what are it's contents?

There isn't that file but I found that there is one in /etc/mysql/my.cnf which is a link from /etc/alternatives/my.cnf Contents of /etc/mysql/mysql.conf.d is: mysqld.cnf mysqld_safe_syslog.cnf

I modified that my.cnf file and comment this line

# thread_concurrency = 8

But the result is still:

root@JWeb:~# dpkg --configure -a
Setting up mysql-server-5.7 (5.7.15-0ubuntu0.16.04.1) ...
Renaming removed key_buffer and myisam-recover options (if present)
ERROR: Unable to start MySQL server:
2016-10-12T06:42:06.803166Z 0 [ERROR] unknown variable 'thread_concurrency=8'
2016-10-12T06:42:06.805823Z 0 [ERROR] Aborting
Please take a look at https://wiki.debian.org/Teams/MySQL/FAQ for tips on fixing common upgrade issues.
Once the problem is resolved, run apt-get --fix-broken install to retry.
dpkg: error processing package mysql-server-5.7 (--configure):
subprocess installed post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of mysql-server:
mysql-server depends on mysql-server-5.7; however:
  Package mysql-server-5.7 is not configured yet.

dpkg: error processing package mysql-server (--configure):
dependency problems - leaving unconfigured
Errors were encountered while processing:
mysql-server-5.7
mysql-server

Updated: I was ablto start MySQL in Virtualmin dashboard and I perform the command dpkg --configure -a again and it worked!

The MySQL upgrade was finished and started. However, I cannot open my website. It always download a "download " file: http://jskill.com/

Here is the apache2 error log:

[Wed Oct 12 06:25:04.652007 2016] [auth_digest:notice] [pid 3697] AH01757: generating secret for digest authentication ...
[Wed Oct 12 06:25:04.669787 2016] [mpm_prefork:notice] [pid 3697] AH00163: Apache/2.4.18 (Ubuntu) SVN/1.9.3 mod_fcgid/2.3.9 OpenSSL/1.0.2g configured -- resuming normal operations
[Wed Oct 12 06:25:04.669797 2016] [core:notice] [pid 3697] AH00094: Command line: '/usr/sbin/apache2'
[Wed Oct 12 07:02:44.638068 2016] [:error] [pid 32208] [client 5.66.150.48:50142] script '/var/www/html/iapentries.php' not found or unable to stat
[Wed Oct 12 07:18:44.764799 2016] [:error] [pid 32180] [client 81.43.7.87:54341] script '/var/www/html/iapentries.php' not found or unable to stat
[Wed Oct 12 07:21:07.566412 2016] [:error] [pid 32180] [client 81.43.7.87:54358] script '/var/www/html/iapentries.php' not found or unable to stat
[Wed Oct 12 07:47:32.347425 2016] [mpm_prefork:notice] [pid 3697] AH00169: caught SIGTERM, shutting down
[Wed Oct 12 07:47:34.488243 2016] [suexec:notice] [pid 42002] AH01232: suEXEC mechanism enabled (wrapper: /usr/lib/apache2/suexec)
[Wed Oct 12 07:47:34.491649 2016] [so:warn] [pid 42002] AH01574: module dav_module is already loaded, skipping
[Wed Oct 12 07:47:34.511235 2016] [auth_digest:notice] [pid 42004] AH01757: generating secret for digest authentication ...
[Wed Oct 12 07:47:34.534407 2016] [mpm_prefork:notice] [pid 42004] AH00163: Apache/2.4.18 (Ubuntu) SVN/1.9.3 mod_fcgid/2.3.9 OpenSSL/1.0.2g configured -- resuming normal operations
[Wed Oct 12 07:47:34.534422 2016] [core:notice] [pid 42004] AH00094: Command line: '/usr/sbin/apache2'
[Wed Oct 12 07:49:28.966378 2016] [:error] [pid 42062] [client 117.83.118.213:5034] script '/var/www/html/iapentries.php' not found or unable to stat
[Wed Oct 12 07:50:29.286205 2016] [:error] [pid 42062] [client 117.83.118.213:5922] script '/var/www/html/iapentries.php' not found or unable to stat

We're glad you got MySQL up and running!

Regarding your website --

I think I know what's going on there... take a look in /etc/apache2/mods-enabled/, is there a file that looks something like "php.ini", or maybe "php7.0.ini"?

If so, edit that file, and look for any line beginning with the word "SetHandler", and then comment that out.

Once that's commented out, restart Apache, and then try accessing your site again. Does it work as expected now?

There is "php7.0.conf" file there and I found those lines. The site was able to be opened. However, there is another error in page:

Internal Server Error

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

Please contact the server administrator at [no address given] 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.

Apache/2.4.18 (Ubuntu) Server at jskill.com Port 80

Apache error log:

[Thu Oct 13 01:33:47.728722 2016] [ssl:warn] [pid 34117] AH01906: jskill.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
[Thu Oct 13 01:33:47.728733 2016] [ssl:warn] [pid 34117] AH01909: jskill.com:443:0 server certificate does NOT include an ID which matches the server name
[Thu Oct 13 01:33:47.785021 2016] [ssl:warn] [pid 34119] AH01906: jskill.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
[Thu Oct 13 01:33:47.785031 2016] [ssl:warn] [pid 34119] AH01909: jskill.com:443:0 server certificate does NOT include an ID which matches the server name
[Thu Oct 13 01:33:59.178134 2016] [fcgid:warn] [pid 34127] (104)Connection reset by peer: [client 115.79.47.73:44035] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 01:33:59.178161 2016] [core:error] [pid 34127] [client 115.79.47.73:44035] End of script output before headers: index.php
[Thu Oct 13 01:33:59.547200 2016] [fcgid:warn] [pid 34194] (104)Connection reset by peer: [client 115.79.47.73:44036] mod_fcgid: error reading data from FastCGI server, referer: http://jskill.com/
[Thu Oct 13 01:33:59.547241 2016] [core:error] [pid 34194] [client 115.79.47.73:44036] End of script output before headers: index.php, referer: http://jskill.com/
[Thu Oct 13 01:34:07.214418 2016] [fcgid:warn] [pid 34127] (104)Connection reset by peer: [client 115.79.47.73:44039] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 01:34:07.214440 2016] [core:error] [pid 34127] [client 115.79.47.73:44039] End of script output before headers: index.php
[Thu Oct 13 01:34:07.412463 2016] [fcgid:warn] [pid 34129] (104)Connection reset by peer: [client 115.79.47.73:44041] mod_fcgid: error reading data from FastCGI server, referer: http://jskill.com/
[Thu Oct 13 01:34:07.412497 2016] [core:error] [pid 34129] [client 115.79.47.73:44041] End of script output before headers: index.php, referer: http://jskill.com/
[Thu Oct 13 01:34:41.606906 2016] [fcgid:warn] [pid 34248] (104)Connection reset by peer: [client 51.255.65.47:28837] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 01:34:41.606928 2016] [core:error] [pid 34248] [client 51.255.65.47:28837] End of script output before headers: index.php

You're receiving a fairly generic error there... I suspect CGI will produce an error message that's more helpful.

To do that, go into Server Configuration -> Website Options, and there, you can set the PHP Execution Mode to "CGI".

Try that, access your website -- and then let us know what error(s) show up in the Apache error logs for that domain.

Website:

Not Found

The requested URL /cgi-bin/php7.0.cgi/index.php was not found on this server.

Apache error log:

[Thu Oct 13 03:08:37.032772 2016] [fcgid:warn] [pid 12171] (104)Connection reset by peer: [client 123.30.175.166:40096] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 03:08:37.032793 2016] [core:error] [pid 12171] [client 123.30.175.166:40096] End of script output before headers: index.php
[Thu Oct 13 03:09:49.628988 2016] [fcgid:warn] [pid 10110] (104)Connection reset by peer: [client 163.172.65.187:32642] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 03:09:49.629009 2016] [core:error] [pid 10110] [client 163.172.65.187:32642] End of script output before headers: index.php
[Thu Oct 13 03:10:20.981811 2016] [fcgid:warn] [pid 12348] (104)Connection reset by peer: [client 203.113.152.8:41125] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 03:10:20.981835 2016] [core:error] [pid 12348] [client 203.113.152.8:41125] End of script output before headers: index.php
[Thu Oct 13 03:10:21.283522 2016] [fcgid:warn] [pid 12171] (104)Connection reset by peer: [client 203.113.152.8:41151] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 03:10:21.283547 2016] [core:error] [pid 12171] [client 203.113.152.8:41151] End of script output before headers: index.php
[Thu Oct 13 03:13:50.717503 2016] [fcgid:warn] [pid 12172] (104)Connection reset by peer: [client 51.255.65.33:32074] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 03:13:50.717525 2016] [core:error] [pid 12172] [client 51.255.65.33:32074] End of script output before headers: index.php
[Thu Oct 13 03:19:30.451829 2016] [fcgid:warn] [pid 10452] (104)Connection reset by peer: [client 164.132.161.85:44850] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 03:19:30.451854 2016] [core:error] [pid 10452] [client 164.132.161.85:44850] End of script output before headers: index.php
[Thu Oct 13 03:22:55.525541 2016] [fcgid:warn] [pid 10450] (104)Connection reset by peer: [client 163.172.66.14:28078] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 03:22:55.525563 2016] [core:error] [pid 10450] [client 163.172.66.14:28078] End of script output before headers: index.php
[Thu Oct 13 03:23:24.571880 2016] [fcgid:warn] [pid 13768] (104)Connection reset by peer: [client 46.101.183.219:39186] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 03:23:24.571898 2016] [core:error] [pid 13768] [client 46.101.183.219:39186] End of script output before headers: index.php
[Thu Oct 13 03:23:24.734036 2016] [fcgid:warn] [pid 13986] (104)Connection reset by peer: [client 46.101.183.219:39202] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 03:23:24.734055 2016] [core:error] [pid 13986] [client 46.101.183.219:39202] End of script output before headers: index.php
[Thu Oct 13 03:27:38.614784 2016] [ssl:warn] [pid 34119] AH01906: jskill.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
[Thu Oct 13 03:27:38.614795 2016] [ssl:warn] [pid 34119] AH01909: jskill.com:443:0 server certificate does NOT include an ID which matches the server name

Try running these commands, and then see if CGI works at that point:

a2enmod cgi
service apache2 restart

Site:

Internal Server Error

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

Please contact the server administrator at [no address given] 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.

Apache/2.4.18 (Ubuntu) Server at jskill.com Port 80

Log:

[Thu Oct 13 06:25:06.274358 2016] [ssl:warn] [pid 34119] AH01906: jskill.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
[Thu Oct 13 06:25:06.274372 2016] [ssl:warn] [pid 34119] AH01909: jskill.com:443:0 server certificate does NOT include an ID which matches the server name
[Thu Oct 13 06:40:28.842955 2016] [ssl:warn] [pid 40464] AH01906: jskill.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
[Thu Oct 13 06:40:28.842968 2016] [ssl:warn] [pid 40464] AH01909: jskill.com:443:0 server certificate does NOT include an ID which matches the server name
[Thu Oct 13 06:40:28.888444 2016] [ssl:warn] [pid 40466] AH01906: jskill.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
[Thu Oct 13 06:40:28.888454 2016] [ssl:warn] [pid 40466] AH01909: jskill.com:443:0 server certificate does NOT include an ID which matches the server name
[Thu Oct 13 06:40:36.803974 2016] [cgi:error] [pid 40485] [client 115.79.47.73:34724] End of script output before headers: php7.0.cgi
[Thu Oct 13 06:40:40.623894 2016] [cgi:error] [pid 40475] [client 115.79.47.73:34727] End of script output before headers: php7.0.cgi
[Thu Oct 13 06:40:42.260437 2016] [cgi:error] [pid 40472] [client 115.79.47.73:34728] End of script output before headers: php7.0.cgi
[Thu Oct 13 06:41:25.075019 2016] [cgi:error] [pid 40472] [client 115.79.47.73:34759] End of script output before headers: php7.0.cgi

It almost seems like PHP in general isn't working properly at the moment -- so maybe the next step is to test PHP.

First, what output do you receive if you run these two commands:

php -v
php-cgi -v

Hi,

root@JWeb:~# php -v
PHP 7.0.8-0ubuntu0.16.04.3 (cli) ( NTS )
Copyright (c) 1997-2016 The PHP Group
Zend Engine v3.0.0, Copyright (c) 1998-2016 Zend Technologies
    with Zend OPcache v7.0.8-0ubuntu0.16.04.3, Copyright (c) 1999-2016, by Zend Technologies
root@JWeb:~# php-cgi -v
The program 'php-cgi' is currently not installed. You can install it by typing:
apt install php7.0-cgi
root@JWeb:~#

Then I installed apt install php7.0-cgi but the issue is still the same.

root@JWeb:~# php-cgi -v
PHP 7.0.8-0ubuntu0.16.04.3 (cgi-fcgi)
Copyright (c) 1997-2016 The PHP Group
Zend Engine v3.0.0, Copyright (c) 1998-2016 Zend Technologies
    with Zend OPcache v7.0.8-0ubuntu0.16.04.3, Copyright (c) 1999-2016, by Zend Technologies

Then I installed:

apt-get install php-mysql

And

sudo apt-get install php-curl

After restarting Apache, some of my sites work back. But jskill.com is still the same. log:

[Thu Oct 13 15:24:18.998350 2016] [core:error] [pid 3885] [client 115.73.29.184:3952] End of script output before headers: test.php
[Thu Oct 13 15:24:19.256643 2016] [fcgid:warn] [pid 3886] (104)Connection reset by peer: [client 115.73.29.184:3960] mod_fcgid: error reading data from FastCGI server, referer: http://jskill.com/test.php
[Thu Oct 13 15:24:19.256695 2016] [core:error] [pid 3886] [client 115.73.29.184:3960] End of script output before headers: index.php, referer: http://jskill.com/test.php
[Thu Oct 13 15:24:20.105604 2016] [fcgid:warn] [pid 3909] (104)Connection reset by peer: [client 115.73.29.184:3959] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 15:24:20.105660 2016] [core:error] [pid 3909] [client 115.73.29.184:3959] End of script output before headers: index.php
[Thu Oct 13 15:24:21.321877 2016] [fcgid:warn] [pid 3884] (104)Connection reset by peer: [client 115.73.29.184:3964] mod_fcgid: error reading data from FastCGI server, referer: http://jskill.com/
[Thu Oct 13 15:24:21.321926 2016] [core:error] [pid 3884] [client 115.73.29.184:3964] End of script output before headers: index.php, referer: http://jskill.com/
[Thu Oct 13 15:24:38.905691 2016] [ssl:warn] [pid 2232] AH01906: jskill.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
[Thu Oct 13 15:24:38.905702 2016] [ssl:warn] [pid 2232] AH01909: jskill.com:443:0 server certificate does NOT include an ID which matches the server name
[Thu Oct 13 15:24:45.749233 2016] [cgi:error] [pid 4475] [client 115.73.29.184:3996] End of script output before headers: php7.0.cgi
[Thu Oct 13 15:24:46.035326 2016] [cgi:error] [pid 4476] [client 115.73.29.184:3997] End of script output before headers: php7.0.cgi, referer: http://jskill.com/
[Thu Oct 13 15:24:51.317960 2016] [cgi:error] [pid 4508] [client 115.73.29.184:3998] End of script output before headers: php7.0.cgi
[Thu Oct 13 15:24:51.959240 2016] [cgi:error] [pid 4507] [client 115.73.29.184:4001] End of script output before headers: php7.0.cgi, referer: http://jskill.com/test.
[Thu Oct 13 15:24:54.101256 2016] [cgi:error] [pid 4475] [client 115.73.29.184:4002] End of script output before headers: php7.0.cgi
[Thu Oct 13 15:24:54.405623 2016] [cgi:error] [pid 4474] [client 115.73.29.184:4004] End of script output before headers: php7.0.cgi, referer: http://jskill.com/test.php

What is the output of this command -- this will ensure that CGI is enabled:

ls /etc/apache2/mods-enabled

If you do see "cgi" in there, can you look at the domain's Apache error log again to ensure that there isn't any additional error output?

Also, one other thing.

Just to rule out other issues -- could you create a file named "test.php" in this domain's public_html folder, and in that file, add the following:

<?php phpinfo(); ?>

Then, try accessing that test.php file in your browser -- what happens when you do that, do you receive an error, or do you see the phpinfo output?

Hi,

As I mentioned above, some of my sites were back like this: http://hero.jskill.com/ But there are some one displaying blank content like this: http://lamgame.vn/

Here is the list:

root@JWeb:~# ls /etc/apache2/mods-enabled
access_compat.load  autoindex.load  filter.load          proxy.load
actions.conf        cgi.load        mime.conf            rewrite.load
actions.load        dav_fs.conf     mime.load            setenvif.conf
alias.conf          dav_fs.load     mpm_prefork.conf     setenvif.load
alias.load          dav.load        mpm_prefork.load     slotmem_shm.load
auth_basic.load     dav_svn.conf    negotiation.conf     socache_shmcb.load
auth_digest.load    dav_svn.load    negotiation.load     ssl.conf
authn_core.load     deflate.conf    php7.0.conf          ssl.load
authn_file.load     deflate.load    php7.0.load          status.conf
authz_core.load     dir.conf        proxy_balancer.conf  status.load
authz_host.load     dir.load        proxy_balancer.load  suexec.load
authz_svn.load      env.load        proxy.conf
authz_user.load     fcgid.conf      proxy_connect.load
autoindex.conf      fcgid.load      proxy_http.load

I cannot run: http://jskill.com/test.php although there is that file in the directort

Apache log

[Thu Oct 13 15:24:18.998350 2016] [core:error] [pid 3885] [client 115.73.29.184:3952] End of script output before headers: test.php
[Thu Oct 13 15:24:19.256643 2016] [fcgid:warn] [pid 3886] (104)Connection reset by peer: [client 115.73.29.184:3960] mod_fcgid: error reading data from FastCGI server, referer: http://jskill.com/test.php
[Thu Oct 13 15:24:19.256695 2016] [core:error] [pid 3886] [client 115.73.29.184:3960] End of script output before headers: index.php, referer: http://jskill.com/test.php
[Thu Oct 13 15:24:20.105604 2016] [fcgid:warn] [pid 3909] (104)Connection reset by peer: [client 115.73.29.184:3959] mod_fcgid: error reading data from FastCGI server
[Thu Oct 13 15:24:20.105660 2016] [core:error] [pid 3909] [client 115.73.29.184:3959] End of script output before headers: index.php
[Thu Oct 13 15:24:21.321877 2016] [fcgid:warn] [pid 3884] (104)Connection reset by peer: [client 115.73.29.184:3964] mod_fcgid: error reading data from FastCGI server, referer: http://jskill.com/
[Thu Oct 13 15:24:21.321926 2016] [core:error] [pid 3884] [client 115.73.29.184:3964] End of script output before headers: index.php, referer: http://jskill.com/
[Thu Oct 13 15:24:38.905691 2016] [ssl:warn] [pid 2232] AH01906: jskill.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
[Thu Oct 13 15:24:38.905702 2016] [ssl:warn] [pid 2232] AH01909: jskill.com:443:0 server certificate does NOT include an ID which matches the server name
[Thu Oct 13 15:24:45.749233 2016] [cgi:error] [pid 4475] [client 115.73.29.184:3996] End of script output before headers: php7.0.cgi
[Thu Oct 13 15:24:46.035326 2016] [cgi:error] [pid 4476] [client 115.73.29.184:3997] End of script output before headers: php7.0.cgi, referer: http://jskill.com/
[Thu Oct 13 15:24:51.317960 2016] [cgi:error] [pid 4508] [client 115.73.29.184:3998] End of script output before headers: php7.0.cgi
[Thu Oct 13 15:24:51.959240 2016] [cgi:error] [pid 4507] [client 115.73.29.184:4001] End of script output before headers: php7.0.cgi, referer: http://jskill.com/test.
[Thu Oct 13 15:24:54.101256 2016] [cgi:error] [pid 4475] [client 115.73.29.184:4002] End of script output before headers: php7.0.cgi
[Thu Oct 13 15:24:54.405623 2016] [cgi:error] [pid 4474] [client 115.73.29.184:4004] End of script output before headers: php7.0.cgi, referer: http://jskill.com/test.php

If that test.php script doesn't work, there's definitely something very odd going on. That script is as simple a PHP app as one can have.

It looks like this particular domain is using FCGID to process that request.

And while that should work, I'm wondering if FCGID is part of the problem you're experiencing.

Could you try changing the jskill.com domain to use CGI as well? I'm curious if using CGI makes any difference at all for the test.php script.

In general, CGI produces much better error messages.

Hi,

Actually I used CGI before. I just tried to switch back to see whether there is difference.

[Thu Oct 13 15:53:05.235802 2016] [ssl:warn] [pid 8730] AH01909: jskill.com:443:0 server certificate does NOT include an ID which matches the server name
[Thu Oct 13 15:53:07.393355 2016] [cgi:error] [pid 8737] [client 115.73.29.184:5271] End of script output before headers: php7.0.cgi
[Thu Oct 13 15:53:07.464045 2016] [cgi:error] [pid 8738] [client 164.132.161.5:55631] End of script output before headers: php7.0.cgi
[Thu Oct 13 15:53:07.777581 2016] [cgi:error] [pid 8735] [client 115.73.29.184:5272] End of script output before headers: php7.0.cgi, referer: http://jskill.com/
[Thu Oct 13 15:54:32.630576 2016] [cgi:error] [pid 8736] [client 163.172.64.227:50690] End of script output before headers: php7.0.cgi
[Thu Oct 13 15:55:07.681081 2016] [cgi:error] [pid 8761] [client 180.76.15.161:28541] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:03:20.364405 2016] [cgi:error] [pid 8735] [client 51.255.65.91:25736] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:05:09.929382 2016] [cgi:error] [pid 8735] [client 115.73.29.184:5999] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:05:10.234744 2016] [cgi:error] [pid 8736] [client 115.73.29.184:6000] End of script output before headers: php7.0.cgi, referer: http://jskill.com/
[Thu Oct 13 16:07:41.827801 2016] [cgi:error] [pid 8736] [client 46.155.29.24:59730] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:07:43.149001 2016] [cgi:error] [pid 8761] [client 46.155.29.24:59716] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:11:46.267477 2016] [cgi:error] [pid 9801] [client 141.212.122.96:15213] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:13:57.846952 2016] [cgi:error] [pid 9814] [client 66.249.64.174:57171] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:15:52.242342 2016] [cgi:error] [pid 10367] [client 220.181.108.120:34662] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:17:44.309055 2016] [cgi:error] [pid 10502] [client 77.75.76.172:14684] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:17:52.247710 2016] [cgi:error] [pid 10502] [client 31.202.247.253:56415] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:19:51.235723 2016] [cgi:error] [pid 8763] [client 163.172.66.6:39756] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:22:12.738633 2016] [cgi:error] [pid 10368] [client 51.255.65.49:26483] End of script output before headers: php7.0.cgi
[Thu Oct 13 16:23:33.843836 2016] [cgi:error] [pid 11293] [client 42.236.10.71:13900] End of script output before headers: php7.0.cgi, referer: http://jskill.com/
[Thu Oct 13 16:25:59.439145 2016] [cgi:error] [pid 11291] [client 163.172.65.24:28720] End of script output before headers: php7.0.cgi

For one of the domain's that's working properly, what is the PHP Execution Mode that the domain is using?

Hrm, that's very puzzling!

Does mod_php work, out of curiosity?

Hrm, that's all very strange. I'm not currently sure what's going on there... I've never seen a case where PHP works for some domains and not others like that.

While I'm thinking about what might be going on there, I'll ask another question -- is the rest of your server working as expected, or are you seeing any other issues?

Hi. I checked and only jskil.com has the issue. Maybe it relates to the SSL issue in the log?

[Thu Oct 13 15:24:38.905691 2016] [ssl:warn] [pid 2232] AH01906: jskill.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
[Thu Oct 13 15:24:38.905702 2016] [ssl:warn] [pid 2232] AH01909: jskill.com:443:0 server certificate does NOT include an ID which matches the server name

I wish it were that simple... but unfortunately those SSL errors are actually normal.

That gives me an idea though... maybe we can just try having it re-generate the Apache config for that domain. Disabling, and then re-enabling, the "Apache website" feature in Virtualmin's "Edit Virtual Server" section would do that.

Does that domain have an SSL certificate though? If so, I believe you'd have to re-add those afterwards, so you may want to keep a copy of the contents of your ssl.cert and ssl.key files located in the home directory.

No we don't use SSL for this domain. Let me make a try.

It didn't work Andreycheck

Is there by chance a .htaccess file in the public_html folder for that domain? If so, can you paste it's contents here?

Hi.

##
# @package    Joomla
# @copyright  Copyright (C) 2005 - 2014 Open Source Matters. All rights reserved.
# @license    GNU General Public License version 2 or later; see LICENSE.txt
##

##
# READ THIS COMPLETELY IF YOU CHOOSE TO USE THIS FILE!
#
# The line just below this section: 'Options +FollowSymLinks' may cause problems
# with some server configurations.  It is required for use of mod_rewrite, but may already
# be set by your server administrator in a way that dissallows changing it in
# your .htaccess file.  If using it causes your server to error out, comment it out (add # to
# beginning of line), reload your site in your browser and test your sef url's.  If they work,
# it has been set by your server administrator and you do not need it set here.
##

## Can be commented out if causes errors, see notes above.
# Options +FollowSymLinks

## Mod_rewrite in use.

RewriteEngine On

## Begin - Rewrite rules to block out some common exploits.
# If you experience problems on your site block out the operations listed below
# This attempts to block the most common type of exploit `attempts` to Joomla!
#
# Block out any script trying to base64_encode data within the URL.
RewriteCond %{QUERY_STRING} base64_encode[^(]*\([^)]*\) [OR]
# Block out any script that includes a <script> tag in URL.
RewriteCond %{QUERY_STRING} (<|%3C)([^s]*s)+cript.*(>|%3E) [NC,OR]
# Block out any script trying to set a PHP GLOBALS variable via URL.
RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
# Block out any script trying to modify a _REQUEST variable via URL.
RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2})
# Return 403 Forbidden header and show the content of the root homepage
RewriteRule .* index.php [F]
#
## End - Rewrite rules to block out some common exploits.

## Begin - Custom redirects
#
# If you need to redirect some pages, or set a canonical non-www to
# www redirect (or vice versa), place that code here. Ensure those
# redirects use the correct RewriteRule syntax and the [R=301,L] flags.
#
## End - Custom redirects

##
# Uncomment following line if your webserver's URL
# is not directly related to physical file paths.
# Update Your Joomla! Directory (just / for root).
##

RewriteBase /

## Begin - Joomla! core SEF Section.
#
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
#
# If the requested path and file is not /index.php and the request
# has not already been internally rewritten to the index.php script
RewriteCond %{REQUEST_URI} !^/index\.php
# and the requested path and file doesn't directly match a physical file
RewriteCond %{REQUEST_FILENAME} !-f
# and the requested path and file doesn't directly match a physical folder
RewriteCond %{REQUEST_FILENAME} !-d
# internally rewrite the request to the index.php script
RewriteRule .* index.php [L]
#
## End - Joomla! core SEF Section.

RewriteCond %{HTTP_HOST} ^www\.(.*)$ [NC]
RewriteRule ^(.*)$ http://%1/$1 [R=301,L]

Hmm, I can't determine at a glance if anything in that might be causing a problem... just for testing purposes, could you rename that to something like .htaccess.orig -- and then try accessing the test.php file that we created earlier?

I'm curious if the test.php works properly at that point.

Hi. Still cannot access that domain. I have a backup of this site before I upgrade Ubuntu and PHP. Should I restore it?

Hi. Still cannot access that domain. I have a backup of this site before I upgrade Ubuntu and PHP. Should I restore it?

It's possible that somehow something with that got corrupted; so yeah maybe trying a backup of that domain would help. Let us know what happens after doing that.

Hi,

Yes it works! Thank you so much.

That's fantastic!

I'm not quite sure what might have gone awry with that, but I'm glad to hear using the backup helped.

Is everything else working as expected now that you've upgraded? Is there anything else we can assist with?