Copy my setup from a non-booting SD card to a fresh USB install

Question

Alright, long story short, I've been running a copy of Raspbian Lite for a while on a RPi 4, off a MicroSD card. I'm using it along with a couple of USB3 drives as a makeshift NAS, where I store my media for my Plex Media Server. It's been running really well for a while, until today.

This evening, I realized it won't boot anymore, and the message I was getting was the ol' "Kernel panic - not syncing: VFS: Unable to mount root fs on unknown-block(179,2)". I've looked it up, been trying to find a way to fix it, but no luck so far. The last thing I've tried is from this thread: Kernel panic-not syncing: VFS: unable to mount root fs on unknown- block(179,6) running Raspbian on top of NOOBS

But I keep bumping into write-protect issues.

I'm not sure at this point if it's fixable, and being the dumb noob I am, I did not have a backup of my SD card...

One thing I picked up on during my research is the ability to boot the RPi from a USB drive. I had an old 120GB SSD collecting dust somewhere, with an enclosure, which should be a lot more stable than a MicroSD card. Using another guide and a fresh install from a different MicroSD than my bad one, I installed Raspbian Lite on the USB SSD, and now it's booting perfectly from it.

With that in mind, I'm now a lot less interested in fixing the old SD card back into functioning if this setup is viable.

Where I'm stuck is: is there way to copy my entire setup, users, programs, mounts, etc... from my "bad" MicroSD, onto my new fresh install on my SSD, effectively making it effectively an exact clone of my old setup, avoiding me from having to set up everything all over again?

I see a lot of guides on how to clone an existing, correctly running install onto a different card or USB drive, but I can't seem to find a guide on how to clone one's setup from a bad, but mountable, readable SD card... I've confirmed that I'm able to mount both partitions in read-only mode, so I have access to all the data.

I have backed up both partitions to separate directories on my SSD install using rsync.

I'm assuming it wouldn't easily be done by just copying all the data onto the corresponding directories on my new install, but hey... wouldn't be nice if it was that easy...

Any thoughts? Thanks in advance

Boot some other SDcard. Stick your broken card in a USB reader and run `sudo umount /dev/sda1; sudo umount /dev/sda2` ignore any errors. Then run `sudo fsck -f -y /dev/sda1;sudo fsck -f -y /dev/sda2`. Power off, swap back to the original SDCard and keep calm and carry on. — Dougie, Jan 16 '21 at 13:13
I'd tried that, but it's complaining about the partition being read-only. I can see that my boot partition might have issues: `0X41: Dirty bit is set. Fs was not properly unmounted and some data may be corrupt`, but it can't run in update mode — ardendolas, Jan 16 '21 at 17:05
Time to toss that SDCard in the bin and start with a factory fresh one. — Dougie, Jan 17 '21 at 00:37

score 1 · Answer 1 · answered Jan 16 '21 at 09:41

1

It's possible that you can repair your SD card with fsck; aka e2fsck & fsck.vfat. There's a recent answer that will walk you through the process. This may not help, but it's not a huge effort - "nothing ventured, nothing gained" as they say. You might also review man e2fsck for background.

Since you are now booting from a USB SSD, you may be able to run fsck with the SD card inserted in the RPi's card slot. Before you do this, make sure the SD card is not mounted - verify this with lsblk --fs.

Good luck & follow up in comments if you have questions.

answered Jan 16 '21 at 09:41

Seamus

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Thanks Seamus, problem is when I try this, the command states my partition is read-only. I ran fsck.vfat on my vfat partition with the -n switch and I get: 'code' 0X41: Dirty bit is set. Fs was not properly unmounted and some data may be corrupt when I run it with the -p switch: open: Read-only file system edit: gah... sorry, can't get the formatting right for the code bits – ardendolas Jan 16 '21 at 16:57
@ardendolas: Sorry that didn't help. I think that [Milliways answer](https://raspberrypi.stackexchange.com/a/120233/83790) is the best approach under these circumstances. The only thing I'd add is this: When using `rsync` in a **recovery** operation such as yours, it may be best to focus on those files and folders containing data thet **you** created - as opposed to a folder such as `/etc` which contains many files whose content was modified **automatically** based on conditions that may not exist on your "restored" system. – Seamus Jan 16 '21 at 19:11
@ardendolas: Looking forward, one other thing: If you decide to try `image-utils` as a backup, [this *step-by-step* may be useful](https://raspberrypi.stackexchange.com/a/120154/83790) – Seamus Jan 16 '21 at 19:14

score 0 · Accepted Answer · answered Jan 16 '21 at 06:41

Do not attempt to apply ANYTHING in that link, which is a different error.

What the message means is partition 2 (of whatever drive contains the root file system) is CORRUPT, or missing.

What you are suggestion may be possible to a sufficiently skilled user, but most wouldn't even attempt this with a faulty OS and creating a bootable SSD is not entirely straightforward.

If you want to attempt recovery you can mount the SD on a linux computer attempt to repair, but this is often not successful and risks further data loss.

Your best bet is to save your data (which you have done) perform a fresh installation on a new SD Card and restore what user data you can recover AND next time make a backup.

I would mount the old SD Card on the new OS (see below script) and use rsync to copy what I could. NOTE this needs to be a selective copy to avoid overwriting the new OS.

#!/bin/bash
BOOT_MOUNT='/mnt/SDA1'
ROOT_MOUNT='/mnt/SDA2'

# Check/create Mount Points
if [ ! -e $BOOT_MOUNT ]; then
    mkdir $BOOT_MOUNT
fi
if [ ! -e $ROOT_MOUNT ]; then
    mkdir $ROOT_MOUNT
fi
    echo "mounts " $BOOT_MOUNT  $ROOT_MOUNT
if [ -e /dev/sda ]; then
    SD1='/dev/sda1'
    SD2='/dev/sda2'
else
    SD1='/dev/sdb1'
    SD2='/dev/sdb2'
fi
echo $SD
# Mount Partitions
if ! $(mountpoint -q $BOOT_MOUNT); then
    mount $SD1 $BOOT_MOUNT  # mount partition containing boot files
fi
if ! $(mountpoint -q $ROOT_MOUNT); then
    mount $SD2 $ROOT_MOUNT  # mount root partition containing OS files
fi

Thanks, I'll look into doing this if I can't repair the SD. Lessons learned! — ardendolas, Jan 16 '21 at 17:23
Actually, I had a question: do you reckon it would work, if I booted off a fresh MicroSD card, then mounted my new USB SSD partitions, and also mounted my busted-but-readable MicroSD in a USB Adapter. Then use `rsync` onto the USB SSD copy? Would that potentially set this SSD as a copy of my old OS, setup and all? I know I'm grasping at straws to avoid a few days' worth of setup to get it back to how I was using it before. Thanks, love the nick and avatar btw! — ardendolas, Jan 18 '21 at 00:34

Copy my setup from a non-booting SD card to a fresh USB install

2 Answers2