Server seems a bit messed up from recent Virtualmin updates

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#1 Sat, 11/24/2012 - 08:08

Server seems a bit messed up from recent Virtualmin updates

I updated all Virtualmin packages, all up date. Now I have issues... the main issue is SSH is not working. It states its running.

SSH from another machine wont accept the password.

Clicking Webmin -> Servers -> SSH Server reports: Failed to get a version number from the SSH server program /usr/sbin/sshd. Maybe your module configuration is incorrect. Output from the command /usr/sbin/sshd -h was :

Clicking Webmin -> Servers -> MySQL Server reports: The MySQL client program /usr/bin/mysql does not appear to be the correct version. Webmin only supports MySQL versions 3 and above.

The command /usr/bin/mysql -V returned

I was going to uninstall SSH but the Software Packages -> Packe Tree does not show anything. Searching for ssh or sshd

Just seems my system is messed up now.

Any ideas where to start, how to fix?

Sat, 11/24/2012 - 08:10

My Config Security & Firewall is enabled but stopped, starting reports this:

open3: exec of perl /etc/csf/ -sf failed at /etc/csf/ line 1642

Sat, 11/24/2012 - 08:12

If I click System and Server Status it states:

HTTP/1.0 500 Perl execution failed Server: MiniServ/1.610 Date: Sat, 24 Nov 2012 14:05:51 GMT Content-type: text/html; Charset=iso-8859-1 Connection: close Error - Perl execution failed

postfix::is_postfix_running failed : Failed to query Postfix config command to get the current value of parameter process_id_directory: at /usr/libexec/webmin/ line 1361.

Sat, 11/24/2012 - 08:18 (Reply to #3)

If I click Re-Check Configuration, I get this:

MySQL does not appear to be installed and running on your system, or has not yet been set up properly in Webmin's MySQL Database module. If your system does not use MySQL, it should be disabled in Virtualmin's module configuration page.

.. your system is not ready for use by Virtualmin.

MySQL was obvioysly working before and in fact the status says its running

Sat, 11/24/2012 - 08:21

I get the feeling anything that requires command line to be run fails. Like command lines wont run or something. Does this make sense? I might be wrong. But a lot of the Virtualmin and Webmin interface works OK, but anything that needs to do some action or report something or run a command seems to fail.

Sat, 11/24/2012 - 21:53


Which Linux distribution/version are you using?

And what is the output of these commands:

ls -l /usr/bin/mysql
ls -l /usr/sbin/sshd
Sun, 11/25/2012 - 03:38

I can't run any commands. I can't login it says password wrong (but its not). I can login to the Virtualmin/Webmin interface though. Running commands in that does nothing.

It's either Centos 6.3

Sun, 11/25/2012 - 17:48

It sounds like you're seeing some pretty serious problems there... nothing like that should ever occur during a package update.

Also, there haven't been any Virtualmin package updates in over a month, so any updates you saw should just have been from your distribution.

Do you know if you have any third party repositories enabled?

You can determine that by going into Webmin -> Others -> Command Shell, and running the command "ls /etc/yum.d/yum.repos.d".

Also, using that same screen, you can run these two commands:

ls -l /usr/bin/mysql
ls -l /usr/sbin/sshd
Mon, 11/26/2012 - 08:05

I cannot run commands...

I was doing this remotely, but I have now managed to get to the machine... the prompt was not working right, no prompt in fact just entering characters and doing nothing. So I hard rebooted the machine.

Now on bootup, half way through loading the OS, I get this:

Kernel Panic - not syncing: attempted to kill init! Pid: 1, comm: switch_root Not tainted 2.6.32-279.14.1.e16.i686 #1 Call trace [there's some trace output here] panic occurred, switching back to text console

Mon, 11/26/2012 - 08:11

P.S. I have not updated it for a while, I run updates every few months maybe. I only have the repos that Virtualmin and/or CentOS would add, I have not added any.

Mon, 11/26/2012 - 09:47

That kernel panic may actually be a sign that you're seeing a hardware issue... quite possibly a hard drive issue.

Performing updates is typically a pretty safe thing to do... it's possible that the problems you saw weren't related to the updates themselves -- but instead, while the updates were installing, if your hard disk was already on it's way out, the updates may have taxed the disk and made the problems apparent.

It sounds like your system currently isn't booting... if you have access to the console, you could always try booting up in failsafe mode (single user mode) to see if you're able to run a fsck on the drive.

However, you may be at a point where it's necessary to fire up a new system, and restore your backups onto it.


Mon, 11/26/2012 - 10:10

I'm not sure about the disk or hardware failing yet as its a fairly new server, only had it for a few months. Its a HP Proliant Server. I use it to take nightly backups of my customers websites. I always test Virtualmin updates on that first before running on all my customers servers. Bit worried about updating the others now.

Actually, could a yum update from the command line break it? Should I always do an update from within Virtualmin? I ask because I think thats what I did.

I am in the process of trying to boot from the Live CD as many have suggested online, then maybe I can run some tests then.

Otherwise I will have to do as you say, put a new drive in, install a new OS, then grab all my files from there.

Mon, 11/26/2012 - 10:31

Like Eric said, it's somewhat unlikely that an update would cause the problems you're seeing now.

To test the HDD, I'd suggest booting into recovery mode, or from a Live CD, and running SMART tests. With SMART you can check if there are found defective sectors, temperature too high, SATA connectivity issues and other things. And you can instruct it to perform a complete read test of the entire drive.

Mon, 11/26/2012 - 12:13

Using "yum update" is actually all Virtualmin is doing from within the UI. And when performing an update on my own server, I typically do it just like you did, from the command line.


Thu, 05/30/2013 - 04:38

I know this is old but I wanted to update this thread.... I decided to reinstall everything at this time (Nov 2011) from scratch again, Centos/Virtualmin... same hardware. Its all been working fine since this issue. Always int he back of my mind when I run updates though!

Sat, 06/15/2013 - 14:47 (Reply to #15)

The problem is not with the Virtualmin update as they suggested. There is a conflict between your kernel and glibc which is what I am currently experiencing. I have a version of glibc which is not compatible with my current distribution of Centos 6.3 and it is causing a conflict and I am not able to run any commands whatsoever so I am searching for ways to reinstall the correct glibc package manually from the src but it is quite difficult. I have the correct rpm of glibc but don't know how to actually install it knowing that the command executions does not work due to the "FATAL: Kernel too old" error.

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