Xubuntu 20.04 disaster

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Xubuntu 20.04 disaster

MR ZenWiz
I need some urgent help here.

After I tried to set the preferred applications on my partner's Dell
laptop, I thought perhaps a software update would be wise.

I ran:

sudo apt -y update
sudo apt -y full-upgrade

All seemed to go well, although there was an error message that looked
harmless enough and I let it go (and don't).

I ran the Software Updater, which updated by removing an older kernel
installation, then said I should reboot.  The two kernel it left
behind were 5.4.0.53 and 5.4.0.54.

Since then, nothing works, in either kernel.  The system only comes up
in emergency boot mode, and a df check shows that the /home filesystem
is completely empty - all her files are gone.

We have a backup from a month or two ago (yes, I know - do it more
often), and we can fall back to there if need be, but I have to say
that this happens too often (radical problems with an update or
emergency reboot) for me to want to continue to use Xubuntu on her
laptop at all.  I never see problems this drastic with my desktop, and
I just don't understand what's going wrong here.

I don't have time to go through how to re-enable the wifi from the
command line - I used to know but it's been long enough that I have to
look it up, and I'm frankly sick and tired of having to go through all
this work, even once a month, just to have a system that runs normally
and reliably - two of the reasons I use Linux to begin with.

If I have to reinstall everything I'll probably go over to Linux Mint
because their system is just plain easier to use (for my partner's
laptop - I don't like Mint and my Xubuntu works fine - so far).

Any positive suggestions would be welcome.  I apologize for letting
out my frustration like this, but I have to leave for PT and can't
even follow up for an hour or so.

Thanks in advance.

Mark

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Re: Xubuntu 20.04 disaster

Colin Law
On Thu, 19 Nov 2020 at 21:48, MR ZenWiz <[hidden email]> wrote:

>
> I need some urgent help here.
>
> After I tried to set the preferred applications on my partner's Dell
> laptop, I thought perhaps a software update would be wise.
>
> I ran:
>
> sudo apt -y update
> sudo apt -y full-upgrade
>
> All seemed to go well, although there was an error message that looked
> harmless enough and I let it go (and don't).
>
> I ran the Software Updater, which updated by removing an older kernel
> installation, then said I should reboot.  The two kernel it left
> behind were 5.4.0.53 and 5.4.0.54.
>
> Since then, nothing works, in either kernel.  The system only comes up
> in emergency boot mode, and a df check shows that the /home filesystem
> is completely empty - all her files are gone.

Do you mean that if you do
ls /home
you see nothing at all?

Does the system have multiple disks or multiple partitions with
systems on them?  Perhaps the system has somehow booted the wrong
system.  Do you get a choice of systems on booting?

Colin

>
> We have a backup from a month or two ago (yes, I know - do it more
> often), and we can fall back to there if need be, but I have to say
> that this happens too often (radical problems with an update or
> emergency reboot) for me to want to continue to use Xubuntu on her
> laptop at all.  I never see problems this drastic with my desktop, and
> I just don't understand what's going wrong here.
>
> I don't have time to go through how to re-enable the wifi from the
> command line - I used to know but it's been long enough that I have to
> look it up, and I'm frankly sick and tired of having to go through all
> this work, even once a month, just to have a system that runs normally
> and reliably - two of the reasons I use Linux to begin with.
>
> If I have to reinstall everything I'll probably go over to Linux Mint
> because their system is just plain easier to use (for my partner's
> laptop - I don't like Mint and my Xubuntu works fine - so far).
>
> Any positive suggestions would be welcome.  I apologize for letting
> out my frustration like this, but I have to leave for PT and can't
> even follow up for an hour or so.
>
> Thanks in advance.
>
> Mark
>
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Re: Xubuntu 20.04 disaster

Karl Auer
In reply to this post by MR ZenWiz
On Thu, 2020-11-19 at 13:46 -0800, MR ZenWiz wrote:
> Since then, nothing works, in either kernel.  The system only comes
> up in emergency boot mode, and a df check shows that the /home
> filesystem is completely empty - all her files are gone.

It would be very unusual for a software update to delete files not
related to the operating system, so I suspect the files are still
there. Use something other than df to make sure - ls is good :-)

I would boot from a USB stick and inspect the system that way. If you
locate the "missing" files, obviously copy them to safety before doing
anything else.

Either way the fastest way back is to re-install from scratch.

And (this is much more for the benefit of others than for you, as you
did mention it): The time between backups is the amount of data you are
prepared to lose. With a current backup, problems like this are no more
than an irritation - re-install, plop the files back, done.

Regards, K.

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Re: Xubuntu 20.04 disaster

Paul Smith-2
In reply to this post by MR ZenWiz
On Thu, 2020-11-19 at 13:46 -0800, MR ZenWiz wrote:
> Since then, nothing works, in either kernel.  The system only comes
> up in emergency boot mode, and a df check shows that the /home
> filesystem is completely empty - all her files are gone.

Almost certainly the files are not gone.

DO NOT REFORMAT!

I'll bet large amounts of money that /home was a separately mounted
partition, and when you boot into emergency boot mode those extra
partitions are not mounted so you just have the empty directory.

Emergency boot mode is DESIGNED to just get you to a minimal system,
and it's even good that it doesn't mount other partitions (just to be
sure they aren't a problem or won't become harmed).

If you run something like:

   cd /
   sudo mount /home

does it work and do the files come back?

Then the question is why the system doesn't boot properly.  To know
that we'd need to know something about what messages you see before it
refuses to boot and dumps you into emergency boot mode.


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Re: Xubuntu 20.04 disaster

MR ZenWiz
In reply to this post by Colin Law
On Thu, Nov 19, 2020 at 1:56 PM Colin Law <[hidden email]> wrote:
>
:
>
> Do you mean that if you do
> ls /home
> you see nothing at all?

My apologies.  No, not quite.  Under /home there were an assortment of
.* directories, but all of the files I knewwere supposed to be there
were not visible, and all the standard directories (Documents,
Downloads, etc.) were also missing.

> Does the system have multiple disks or multiple partitions with
> systems on them?  Perhaps the system has somehow booted the wrong
> system.  Do you get a choice of systems on booting?
>

Unfortunately, no.  I had to reinstall this system from scratch about
5 months ago.  I was able to back up all the files and restore them
after the reinstall, but I did one stupid thing (or one too many...) -
I did not divide the disk into a separate home partition, which I
absolutely will do if I need to reinstall this time, or maybe just
anyway.

The good news so far is that I rebooted from my install USB stick and
all the files appear to be visible.  I am backing them up to an
external hard drive as I write this, then I can proceed with further
recovery, secure in knowing that her files are (almost certainly)
safe(r).

What bugs me is that the hard drive boot could not see the files at
all.  I'm not sure how that's possible.

Thanks.

Mark

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Re: Xubuntu 20.04 disaster

MR ZenWiz
In reply to this post by Paul Smith-2
On Thu, Nov 19, 2020 at 2:40 PM Paul Smith <[hidden email]> wrote:
>
:
> Almost certainly the files are not gone.
>
> DO NOT REFORMAT!
>
Not unless there was no other option whatsoever.

> I'll bet large amounts of money that /home was a separately mounted
> partition, and when you boot into emergency boot mode those extra
> partitions are not mounted so you just have the empty directory.
>
As I just posted, unfortunately not.  I used the default disk format
when I reinstalled the OS back in June.  I'll never do that again.

I never do that on my machine, but that's mainly because I run off an
SSD, which holds / and nothing else.  /home is on a separate, much
larger hard disk.

> Emergency boot mode is DESIGNED to just get you to a minimal system,
> and it's even good that it doesn't mount other partitions (just to be
> sure they aren't a problem or won't become harmed).
>
> If you run something like:
>
>    cd /
>    sudo mount /home
>
> does it work and do the files come back?
>
I will try that when the backup is complete.

> Then the question is why the system doesn't boot properly.  To know
> that we'd need to know something about what messages you see before it
> refuses to boot and dumps you into emergency boot mode.
>
I'll post them (and not let them get away) next time I boot the
machine.  I remember an fsck report, but there was more I don't
recall.

Coming soon...

Thanks!

Mark

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Re: Xubuntu 20.04 disaster

MR ZenWiz
In reply to this post by Karl Auer
On Thu, Nov 19, 2020 at 2:09 PM Karl Auer <[hidden email]> wrote:
>
:
>
> It would be very unusual for a software update to delete files not
> related to the operating system, so I suspect the files are still
> there. Use something other than df to make sure - ls is good :-)
>
I did, though I failed to say so.  Thanks for pointing that out.

> I would boot from a USB stick and inspect the system that way. If you
> locate the "missing" files, obviously copy them to safety before doing
> anything else.
>
Underway.

> Either way the fastest way back is to re-install from scratch.
>
I probably will.  It's easier than most other options, but what a
pain.  I shudder to think how an inexperienced newbie to Linux might
respond if this happened to them.  Ick.

> And (this is much more for the benefit of others than for you, as you
> did mention it): The time between backups is the amount of data you are
> prepared to lose. With a current backup, problems like this are no more
> than an irritation - re-install, plop the files back, done.
>
And I should be well aware of that, having painfully been forced to do
things like this before.

When I reinstalled the system, this is exactly what I did - boot from
a DVD, backup all the files to an external hard drive, reinstall and
restore the files.

Not sure why I didn't absorb this well enough to avoid making the same
dumb mistake last time around.  Never again.  Never!

Thanks.

Mark

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Re: Xubuntu 20.04 disaster

ubuntu-users mailing list
In reply to this post by MR ZenWiz
On Thu, 19 Nov 2020 17:24:33 -0800, MR ZenWiz wrote:
>> If you run something like:
>>
>>    cd /
>>    sudo mount /home
>>
>> does it work and do the files come back?
>>  
>I will try that when the backup is complete.

That /home isn't mounted was my first and only guess, too.
The only thing else I can imagine is a package installed by a third
party repository was running a malicious script.

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Re: Xubuntu 20.04 disaster

MR ZenWiz
On Thu, Nov 19, 2020 at 6:22 PM Ralf Mardorf via ubuntu-users
<[hidden email]> wrote:

>
> On Thu, 19 Nov 2020 17:24:33 -0800, MR ZenWiz wrote:
> >> If you run something like:
> >>
> >>    cd /
> >>    sudo mount /home
> >>
> >> does it work and do the files come back?
> >>
> >I will try that when the backup is complete.
>
> That /home isn't mounted was my first and only guess, too.
> The only thing else I can imagine is a package installed by a third
> party repository was running a malicious script.
>
My sincerest apologies.  I have been having brain farts a lot since I
came out of a COVID coma seven months ago.

The disk was in fact partitioned properly - one for root and one for
/home.  /home was corrupted (a bunch of files needed fixed), but I a)
completely forgot I made this intelligent move when I reinstalled the
OS back in June, and b) didn't notice when I ran gparted from the
Xubuntu boot flash drive live that there were two ext4 partitions on
the hard drive, not only 1.  Not quite sure how that escaped my
notice.

When I reinstalled, the system still refused to come up - after I
modified /etc/fstab to bring up /home on the correct partition.  At
that point I finally realized what was going on and ran fsck on /home,
and there were a bunch of errors that got fixed.  After that, the
reboot worked properly and is happily humming away.

Here are some things I notice now in retrospect:

1) This was an upgraded system that failed.  Still not sure why.
2) Before the failure, LibreOffice was not starting up properly -
something was interfering with it coming up, and running it from the
command line did not show me anything I recognized as problematic.
3) Chrome was already set to the default browser, but it wasn't
starting up properly (all indirect starts brought up Firefox and I
couldn't modify this).
4) I'm not sure why the file system was so corrupt, but apparently the
update and full-upgrade triggered something that precipitated this
result.

Thank you to all who responded.  I have learned once again that Linux
distros can be easy to fix when something goes wrong, assuming that
the admin doesn't lose his marbles and forget some basic, however
intricate, precautions have been set up (and then fails to notice them
when he is flailing around trying not to drown on dry land).

Two points for Linux and minus ten for me.  I'll have to earn them back...

Thanks to all for your patience and kind assistance.  I should know
better - I've been doing home Linux sysadmin work for almost 14 years
straight now, 10 in X/Ubuntu

Mark

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Re: Xubuntu 20.04 disaster

Tom H-4
In reply to this post by MR ZenWiz
On Fri, Nov 20, 2020 at 2:30 AM MR ZenWiz <[hidden email]> wrote:
>
> I shudder to think how an inexperienced newbie to Linux might
> respond if this happened to them.

Let's not start panicking.

1) No software's bug free.

2) LTS-to-LTS upgrades are bound to fail from time to time.

3) Newbies are more likely to install than to upgrade.

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Re: Xubuntu 20.04 disaster

Chris Green
In reply to this post by Paul Smith-2
On Thu, Nov 19, 2020 at 05:38:51PM -0500, Paul Smith wrote:
> On Thu, 2020-11-19 at 13:46 -0800, MR ZenWiz wrote:
>
> If you run something like:
>
>    cd /
>    sudo mount /home
>
I think that may need a device to mount as well:-

    sudo mount /dev/sdxx /home

It depends if there's access to the original /etc/fstab or not.

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Re: Xubuntu 20.04 disaster

Peter Flynn
In reply to this post by Tom H-4
On 20/11/2020 09:20, Tom H wrote:
> 3) Newbies are more likely to install than to upgrade.

Oldies always install, never upgrade :-)

P

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Re: Xubuntu 20.04 disaster

Colin Law
In reply to this post by MR ZenWiz
On Fri, 20 Nov 2020 at 06:06, MR ZenWiz <[hidden email]> wrote:
>  At
> that point I finally realized what was going on and ran fsck on /home,
> and there were a bunch of errors that got fixed.  After that, the
> reboot worked properly and is happily humming away.

That comment, plus all the strange other symptoms you describe with
libreoffice etc lead me to suspect you might have a dodgy disc.  I
suggest checking the SMART data for the disc. Don't ask me how, I
always have to google it on the rare occasions I need it.  If that
shows ok then have a look in syslog to see if there are any possibly
related messages there.  If the disc is not dying then it may be you
have corrupted some system files somehow.  The machine wasn't right
before the upgrade so the problems may just have been shown up by the
upgrade rather than caused by it.

Colin

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Re: Xubuntu 20.04 disaster

Colin Law
In reply to this post by Peter Flynn
On Fri, 20 Nov 2020 at 11:24, Peter Flynn <[hidden email]> wrote:
>
> On 20/11/2020 09:20, Tom H wrote:
> > 3) Newbies are more likely to install than to upgrade.
>
> Oldies always install, never upgrade :-)

Not true, assuming being past the statutory six score years and ten
counts as old.  I always upgrade unless there is a particular issue
forcing a re-install.

Colin

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Re: Xubuntu 20.04 disaster

Chris Green
In reply to this post by Peter Flynn
On Fri, Nov 20, 2020 at 11:23:00AM +0000, Peter Flynn wrote:
> On 20/11/2020 09:20, Tom H wrote:
> > 3) Newbies are more likely to install than to upgrade.
>
> Oldies always install, never upgrade :-)
>
Not true! :-)

I think I took my desktop system from somewhere around 10.04 to 18.04
before doing a re-install.  Even then I only re-installed because I
had added a new NVME disk and it was easier to make a new installation
on the new disk and then copy stuff across as needed. It was quite an
exercise in boot reconfiguration because the new NVME disk wasn't seen
by the BIOS, otherwise I would probably have continued upgrading.

The big advantage of upgrading is that one doesn't have to remember
all the extra packages one has installed, plus any OS customisation.
Of course that's also the disadvantage, you get to keep all that stuff
you added that you no longer need! :-)

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Re: Xubuntu 20.04 disaster

Peter Flynn
On 20/11/2020 11:51, Chris Green wrote:
> On Fri, Nov 20, 2020 at 11:23:00AM +0000, Peter Flynn wrote:
[...]
>> Oldies always install, never upgrade :-)
>>
> Not true! :-)
> I think I took my desktop system from somewhere around 10.04 to 18.04
> before doing a re-install.

On 20/11/2020 11:32, Colin Law wrote:
 > Not true, assuming being past the statutory six score years and ten
 > counts as old.  I always upgrade unless there is a particular issue
 > forcing a re-install.

OK, I'll bow out on that 😀 but having been bitten twice by serious bugs
in distribution upgrades I have always gone from scratch for safety.
> The big advantage of upgrading is that one doesn't have to remember
> all the extra packages one has installed, plus any OS customisation.

By now I have a well-tried shell script that does all this in the right
order, so I basically kick it off and go for dinner.

I do rely on the OS leaving /home alone, and on production systems
/var/sys is always a separate spindle, so that gets unplugged before the
installation, and added back later (very large quantities).

P

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Re: Xubuntu 20.04 disaster

Liam Proven
In reply to this post by Colin Law
On Fri, 20 Nov 2020 at 12:34, Colin Law <[hidden email]> wrote:
>
> Not true, assuming being past the statutory six score years and ten
> counts as old.

Six score and ten?! You are 130? Wow! In that case, I cheerfully
concede that you are the oldest Linux user in the world, already being
a centenarian when Linus first published his source code. You have
also exceeded Jean Calment's tally and must be the world's oldest
person.

>   I always upgrade unless there is a particular issue
> forcing a re-install.

Me too, as a mere stripling of 53 who has only been using Linux for
half their life.

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Re: Xubuntu 20.04 disaster

Paul Smith-2
In reply to this post by Chris Green
On Fri, 2020-11-20 at 09:22 +0000, Chris Green wrote:
> I think that may need a device to mount as well:-
>
>     sudo mount /dev/sdxx /home
>
> It depends if there's access to the original /etc/fstab or not.

Since the system booted up on the original root partition I expect that
/etc/fstab was still present and correct.

Certainly after the OS has been re-installed and the fstab is lost
you'll need to use the longer form.


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Re: Xubuntu 20.04 disaster

Colin Law
In reply to this post by Liam Proven
On Fri, 20 Nov 2020 at 12:15, Liam Proven <[hidden email]> wrote:
>
> On Fri, 20 Nov 2020 at 12:34, Colin Law <[hidden email]> wrote:
> >
> > Not true, assuming being past the statutory six score years and ten
> > counts as old.
>
> Six score and ten?! You are 130?

Oops, that's what comes from doing a maths degree, great at the theory
but rubbish at the practice :)
Plus being a little while ago I'm not so good at the theory either.

Colin

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Re: Xubuntu 20.04 disaster

Liam Proven
On Fri, 20 Nov 2020 at 16:00, Colin Law <[hidden email]> wrote:

> Oops, that's what comes from doing a maths degree, great at the theory
> but rubbish at the practice :)
> Plus being a little while ago I'm not so good at the theory either.

:-D

"In theory, there's no difference between theory and practice. In
practice, there is."

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