I did something wrong with 20.04]

[Gnusboy]

Hey all

In my effort to get my system working after the trouble I had with the suspicious file mentioned earlier
See https://ubuntuforums.org/showthread.php?t=2464806

I might have mucked up my file system and lost some important files. It appears that my main root filesystem has a lot wrong. I could sure use help to figure it all out.


The background to this is a mouse the kept freezing, then releasing, etc. but then locked up to the point of having to reboot to make it work. This problem led me to attempt a fix using FSCK. But I didn't read the part where I was supposed to do this from root w/o mounted file systems. I tried that twice and it then came back with "error code 2."
I tried to run fsck again, but then the system came back with the BusyBox v1.30.1 Initramfs errors. I read as much as I could on how to proceed, but didn't see any solution that I thought fit my situation.
Finally, I rebooted with the 20.04 live disk and to "Try Ubuntu" That brought up 2 partitions - one empty and the other with the file systems I had been using.
I checked on my documents - which seemed OK, but I'm not sure I still had all of them.
I don't recall exactly what I did then, but there was a banner showing
Circle X Access with sys/device/software/subsystem/uevent denied
I hit OK and the banner closed
In the second partition (supposedly empty) There was a file labeled
"Ubiquity Desktop"name:~desktop/ubiquity.desktop
2[read only] /run/network manager/devices

Failed to start shuts down pre-installed sys cleanly
SystemCTL i status Casper.service for detail
OK Reached Target Final step/finished powered-off
OK Finished reached target power off
[!!!!!!] Failed Execute shutdown binary [40985.213694] blk_update_request] I/O Error
Plus several similar lines.

Earlier today the screen was frozen and I did a soft reboot and got
Begin: running/scripts/local-premount ... done
Begin: Will now check root file system ... fsck from util-linux 2.34 [/usr/sbin/fsck.ext4 (1) --/dev/sda5] fsck,ext4 -a -C0 /dev/sda5 /dev/sda5 contains a file system with errors, check forced
[ 10.326632] random: crng init done ==== \54.4% /dev/sda5:
Inode 35401772 extent tree (at level 1) could be shorter. IGNORED. /dev/sda5: Inodeds that were part of a corrupted orphan linked list found.
/dev/sda5: UNEXPECTED INCONSISTENCY; RUN fsck MANUALLY (I.E., WITHOUT -A OR -P OPTIONS
fsck exited with status code 4 done.
FAILURE: file system check of the root filesystem failed
the root filesystem on /dev/sda5 requires a manual fsck

BusyBox /
(initramfs)

Thanks

[yancek]

What happened when you did the manual fsck recommended? Should be able to find lots of sites explaining how to do this on Linux/Ubuntu.

[TheFu]

To manually do an fsck, there are a few different ways. In the boot menu, there's an "Advance .... " something on the list of kernels. Select that. Then pick one of the "Recovery Mode" choices. That will boot a RAM-only environment and I think it brings up a blue/red screen with a menu of options. One of the options is "Run fsck on all file systems" or perhaps "Check all file systems" - pick that.

The other easy way is to boot from any Ubuntu Desktop flavor ISO (usually a flash drive), go into "Try Ubuntu" mode, then open a terminal and run fsck manually on all the partitions and LVs with file systems. Not all partitions will have file systems, so it would be good to know the size and device names of those that do. Don't run fsck on any swap, for example. Also, if you use LVM or chose an encrypted system at install time, then there are more details since the sda3 partition (the usual device where LVM stuff gets placed) doesn't have a file system to check.

If you get stuck, run

lsblk -e 7 -o name,size,type,fstype,mountpoint

inside the Live-Boot/Try Ubuntu environment and post the results here with the command AND results wrapped in code-tags. Https://ubuntuforums.org/misc.php?do=bbcode#code explains code-tags.

[Gnusboy]

I didn't want to run an fsck until I was sure I wouldn't do the wrong thing. When I saw corrupted orphan and the root filesystem failed. etc.
I have the 20.04 on a disk. So I start that until I get to Try Ubuntu, click that and let it load, run fsck. Right?
Is the recovery fsck on all filesystems, if that option is available, the same as running manual fsck individually?
Then I'll post whatever shows on the results, OK?
I only have 2 partitions on the drive and one of those is empty. I believe /dev/sda5 is where everything is inside.the so it should be pretty quit. My main concern is whether I have lost any documents. I have a lot of time and work sitting inside those
files.
BTW what is LVM?

[TheFu]

Try it. See what happens. The maintenance mode version takes the guesswork away, so that would be much easier for most people to use.

If you are worried about lost documents, then clearly your backup process needs work. Fix that ASAP.

[Gnusboy]

Yeah, I'm always behind on backups. Until recently, I backup most of my work on an external drive. I disconnected it a couple of months ago - I don't recall why. I may have paid the price for that.
Given the status of my current system, is there a way to copy my existing files over to the external drive?
Or, do I need to wait it out until its repaired?

I didn't want to run an fsck until I was sure I wouldn't do the wrong thing. When I saw corrupted orphan and the root filesystem failed. etc.

I have the 20.04 on a disk. So I start that until I get to Try Ubuntu, click that and let it load, run fsck. Right?
Is the recovery fsck on all filesystems, if that option is available, the same as running manual fsck individually?
Then I'll post whatever shows on the results, OK?
I only have 2 partitions on the drive and one of those is empty. I believe /dev/sda5 is where everything is inside.the so it should be pretty quit. My main concern is whether I have lost any documents. I have a lot of time and work sitting inside those
files.
BTW what is LVM?

OK.As soon as I hit EXIT from initramfs, it ran fsck manually on the root file system, it showed [/user/sbin/fsck.ext4 (1) --/dev/dev/sda5] fsck.ext4 -a -CO ./dev/sda5 contains the file system with errors, check forced.
I will let you know what happens.
And thank you for your help.

[ActionParsnip]

If your documents are important... You have made a backup of them.... Right?

[TheFu]

If you get stuck, run the command in #3 above and post the outputs. Then we can easily tell if you need to care about LVM or not. Either you have it or your don't. Most of the time, people would absolutely KNOW they picked to use LVM for storage management. But sometimes people don't read the monitor and get it without understanding.

I bet there's a wikipedia article on LVM if you want an overview. In LVM, partitions aren't where file systems get placed, so you will see partitions, but won't be able to click to open them directly.

I like LVM for flexibility. But it does add some complexity to storage management. Most people who don't do enterprise storage would probably not choose LVM. However, in the Ubuntu installers, if encrypted storage is picked, then they use LVM as well. This isn't mandatory, but it is smart, IMHO.

[Gnusboy]

thanks for getting rid of those extra paragraphs. I didn't see them until later.

[Gnusboy]

The difference between, I know I should, and yeah I did, is vast.
I kept having problems with Deja-Dup. Sometimes it worked and other times not. I kept telling myself to get a different
backup program, but it was a low priority. However, when I get my system back up, I'll get one asap
I did have some backups. I don't recall from when.
So if I don't have the most recent, I can probably rework them.