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#1 2019-09-06 22:46:54

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
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Accidentally re-formatted boot sector :-(

So this is one of those things that happen after a long work week. I intended to re-format a pen-drive but accidentally re-formatted a boot sector on my HDD. Right now I am running a back-up of everything in the user space of this computer.

All may not be doom and gloom as I have two HDDs in this machine and boot sectors ar RAIDed for redundancy. All in all my partitioning scheme looks like this:

/dev/sda

  part        filesys     mount   size      comments
  /dev/sda1   ext4                0,2 GiB   boot, part of RAID1 md0
  /dev/sda2   linux-swap          1,0 GiB   swap, part of RAID0 md1
  /dev/sda3   extended            499 GiB
  /dev/sda5   btrfs       /       9,77 GiB  system, btrfs RAID(1/0)
  /dev/sda6   btrfs       /home   400 GiB   user space, btrfs RAID(0/0)
  /dev/sda7   ext4        /extra  55,6 GiB  VMs etc, part of RAID0 md2


/dev/sdb

  part        filesys     mount   size      comments
  /dev/sdb1   ext4                0,2 GiB   boot, part of RAID1 md0
  /dev/sdb2   linux-swap          1,0 GiB   swap, part of RAID0 md1
  /dev/sdb3   extended            499 GiB
  /dev/sdb5   btrfs       /       9,77 GiB  system, btrfs RAID(1/0)
  /dev/sdb6   btrfs       /home   400 GiB   user space, btrfs RAID(0/0)
  /dev/sdb7   ext4        /extra  55,6 GiB  VMs etc, part of RAID0 md2

Am I right in thinking that the RAID set-up may help me save me from a complete re-install? If yes, I would appreciate a step-by-step guide (here or a link to) to recovery.

TIA,

/Martin (time to go to bed)

Last edited by Martin (2019-09-07 09:16:37)


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#2 2019-09-07 09:18:23

Martin
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Re: Accidentally re-formatted boot sector :-(

No takers?

In the mean time I study what the ArchWiki has to say about RAID.

/Martin


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#3 2019-09-07 13:43:43

eight.bit.al
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Re: Accidentally re-formatted boot sector :-(

I'll take a stab at it, as this is an area I have experience in breaking. sad

I think you mean boot partition, instead of boot sector. Image. Is that correct?

The goal of redundant RAID is if one drive dies the other (in your case two drives) contains a viable copy. Necessarily, what gets written to one drive gets written to the other, including a format.

A lot depends where the GRUB folder, kernel images,  initrd.img, etc were/are stored. I'm guessing /dev/sda1.

Try Rescatux, and/or Super Grub2 Disk, if only to try and boot into your Linux system and restore from there. Good luck.

8bit

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Last edited by eight.bit.al (2019-09-07 13:44:18)

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#4 2019-09-07 13:58:08

Martin
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From: Stockholm, Sweden
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Re: Accidentally re-formatted boot sector :-(

Hmm, I start to suspect, strongly suspech, that what I abused yesterday was not a disk partition but rather md0 -- RAID1 does not help me then I guess.

I haven't touched anything yet but mdadm indicates md0 is still a working RAID1 set-up. One reason for worry is that it shows up as non-mounted 'disk' in Thunar. It never did that before!

Also, I just ran an up-date in Synaptic and there is a bunch of error messages I don't think I have seen in the past:

cryptsetup: WARNING: failed to detect canonical device of /dev/sda5
cryptsetup: WARNING: failed to detect canonical device of /dev/sdb5
cryptsetup: WARNING: could not determine root device from /etc/fstab

So it fails to find my root partition(s).

For now I try not to switch off or re-boot and continue research hoping I will not have to re-install Helium from scratch.

/Martin


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#5 2019-09-07 14:40:20

eight.bit.al
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Re: Accidentally re-formatted boot sector :-(

Can you go back in your BASH history, or whatever shell, and paste the command you used to "format" for us to look at?

8bit

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    - Voltaire (1694-1778) on his deathbed in response to a priest asking that he renounce Satan.

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#6 2019-09-07 18:47:52

Martin
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Re: Accidentally re-formatted boot sector :-(

I used GParted...

It is a pity Lithium is not ready for prime time as it seems I created the perfect excuse for moving on from Helium.

/Martin

Last edited by Martin (2019-09-07 21:16:49)


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#7 2019-09-07 21:30:03

beaker
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Re: Accidentally re-formatted boot sector :-(

If the setup is correct and it is raided for redundancy (as you said) you should be fine and it will survive the reboot. If it is raided for speed then you will not be fine.

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#8 2019-09-07 21:59:24

Martin
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Re: Accidentally re-formatted boot sector :-(

This looks like a good process if I have indeed wiped md0 and need to re-install Grub (or have I misunderstood how these things work???). Since I have not shut down or re-booted my computer (posting from it now) I assume I could go to step 8 and do:

grub-install --root-directory=/ /dev/sda

without the need for a Live-CD?

Right??

/Martin

Last edited by Martin (2019-09-07 22:00:17)


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#9 2019-09-07 22:21:30

eight.bit.al
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Re: Accidentally re-formatted boot sector :-(

Suggestion:

run GParted, grab a screenshot and post results.

8bit

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#10 2019-09-08 08:10:22

Martin
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Re: Accidentally re-formatted boot sector :-(

This is what GParted looks like when studying md0 (now back to ext4 from a temporary fat32 life):
GParted md0

I notice there is an "Attempt Data Rescue" instance in the "Device" menu. Worth trying?

/Martin


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#11 2019-09-08 11:29:31

eight.bit.al
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Re: Accidentally re-formatted boot sector :-(

^ Not as helpful as hoped for. So little data on /dev/md0, 11.83 MiB, this is / and I would expect a lot more.
This looks like normal space reserved by the file system more than actual data.

Martin wrote:

(now back to ext4 from a temporary fat32 life)

an up-date in Synaptic

And too many moving parts. This is a whole other conversation; how did you do the conversion, etc.
The first rule of "file system errors" is to do as little as possible.

I notice there is an "Attempt Data Rescue" instance in the "Device" menu. Worth trying?

I think that's more for simple errors (restoring a deleted partition type error) than anything more serious.

So many questions and no access to the machine, it's hard to say...

cryptsetup: WARNING: could not determine root device from /etc/fstab

Does the UUID in fstab match the UUID of the actual partition?
And so forth...


Hey Devs, we have a motivated alpha tester here! smile

8bit

I have no special talent. I am only passionately curious. - Albert Einstein

Last edited by eight.bit.al (2019-09-08 11:40:47)

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#12 2019-09-08 11:54:03

rbh
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Re: Accidentally re-formatted boot sector :-(

Martin wrote:

I notice there is an "Attempt Data Rescue" instance in the "Device" menu. Worth trying?
/Martin

Your partitionscheme in the first post, is that output from an command (if so, which) or list of how it was once?
Do you remeber if you set upp raid0 or raid1?
The swap should not be mirrored (raid1), it should be raid0.
The /home looks suspicious with "RAID(0/0)".

The output from:

# lsblk -f
and
# mdadm --detail /dev/md*

would give information enough to proceed.

Last edited by rbh (2019-09-08 12:16:13)


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#13 2019-09-08 12:14:36

rbh
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Re: Accidentally re-formatted boot sector :-(

Martin wrote:

md0 (now back to ext4 from a temporary fat32 life):

I missed this before. Did you convert fat32>ext4 now after your missfortune?
Why did you convert it? The size and partitiontype hints that it is an uefi-partion. UEFI partition must be in fat to support booting.

If you have the time to spare, you can try to fix your missfortune, else it might be better to reinstall.

You can install Helium and upgrade to buster/lithium-dev.

Last edited by rbh (2019-09-08 12:15:12)


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#14 2019-09-08 12:55:14

eight.bit.al
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Re: Accidentally re-formatted boot sector :-(

^
Wheeew. Finally someone who sounds like they know what their talking about.  smile

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#15 2019-09-08 14:21:42

Martin
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From: Stockholm, Sweden
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Posts: 351
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Re: Accidentally re-formatted boot sector :-(

rbh wrote:
Martin wrote:

I notice there is an "Attempt Data Rescue" instance in the "Device" menu. Worth trying?
/Martin

Your partitionscheme in the first post, is that output from an command (if so, which) or list of how it was once?
Do you remeber if you set upp raid0 or raid1?
The swap should not be mirrored (raid1), it should be raid0.
The /home looks suspicious with "RAID(0/0)".

The table in the first post shows what it all looked like after building the system in December last year.

rbh wrote:

The output from:

# lsblk -f
and
# mdadm --detail /dev/md*

would give information enough to proceed.

martin@he2:~$ lsblk -f
NAME    FSTYPE            LABEL UUID                                 MOUNTPOINT
sda                                                                  
├─sda1  linux_raid_member he2:0 f8d3a77f-8a8d-c09e-2535-1387b1a0d42d 
│ └─md0 ext4                    4666049c-8f1e-4f0d-89bc-10d8e14a5a6c 
├─sda2  linux_raid_member he2:1 4bcd4789-cb0b-b8f2-ba5a-47f71e3e0cd8 
│ └─md1 swap                    89c3dd1a-ed27-4b77-8c29-a2cc9e599a96 [SWAP]
├─sda5  btrfs                   d112bfbd-53ca-4d8e-a8a9-f7a4b5d15f52 /
├─sda6  btrfs                   84136c02-e53e-43f6-b5d2-85999816add0 /home
└─sda7  linux_raid_member he2:2 b1343f78-6b8d-1f99-211f-073d323d1683 
  └─md2 ext4                    f0210d74-89ad-46c8-ba11-c91b9245bedd /extra
sdb                                                                  
├─sdb1  linux_raid_member he2:0 f8d3a77f-8a8d-c09e-2535-1387b1a0d42d 
│ └─md0 ext4                    4666049c-8f1e-4f0d-89bc-10d8e14a5a6c 
├─sdb2  linux_raid_member he2:1 4bcd4789-cb0b-b8f2-ba5a-47f71e3e0cd8 
│ └─md1 swap                    89c3dd1a-ed27-4b77-8c29-a2cc9e599a96 [SWAP]
├─sdb5  btrfs                   d112bfbd-53ca-4d8e-a8a9-f7a4b5d15f52 
├─sdb6  btrfs                   84136c02-e53e-43f6-b5d2-85999816add0 
└─sdb7  linux_raid_member he2:2 b1343f78-6b8d-1f99-211f-073d323d1683 
  └─md2 ext4                    f0210d74-89ad-46c8-ba11-c91b9245bedd /extra
sr0                     

and

martin@he2:~$ sudo mdadm --detail /dev/md*
[sudo] lösenord för martin: 
mdadm: /dev/md does not appear to be an md device
/dev/md0:
        Version : 1.2
  Creation Time : Sat Dec  8 11:38:44 2018
     Raid Level : raid1
     Array Size : 204608 (199.81 MiB 209.52 MB)
  Used Dev Size : 204608 (199.81 MiB 209.52 MB)
   Raid Devices : 2
  Total Devices : 2
    Persistence : Superblock is persistent

    Update Time : Sun Sep  8 10:00:44 2019
          State : clean 
 Active Devices : 2
Working Devices : 2
 Failed Devices : 0
  Spare Devices : 0

           Name : he2:0  (local to host he2)
           UUID : f8d3a77f:8a8dc09e:25351387:b1a0d42d
         Events : 1084

    Number   Major   Minor   RaidDevice State
       0       8        1        0      active sync   /dev/sda1
       1       8       17        1      active sync   /dev/sdb1
/dev/md1:
        Version : 1.2
  Creation Time : Sat Dec  8 11:39:15 2018
     Raid Level : raid0
     Array Size : 2045952 (1998.00 MiB 2095.05 MB)
   Raid Devices : 2
  Total Devices : 2
    Persistence : Superblock is persistent

    Update Time : Sat Dec  8 11:39:15 2018
          State : clean 
 Active Devices : 2
Working Devices : 2
 Failed Devices : 0
  Spare Devices : 0

     Chunk Size : 512K

           Name : he2:1  (local to host he2)
           UUID : 4bcd4789:cb0bb8f2:ba5a47f7:1e3e0cd8
         Events : 0

    Number   Major   Minor   RaidDevice State
       0       8        2        0      active sync   /dev/sda2
       1       8       18        1      active sync   /dev/sdb2
/dev/md2:
        Version : 1.2
  Creation Time : Sat Dec  8 11:39:47 2018
     Raid Level : raid0
     Array Size : 114081792 (108.80 GiB 116.82 GB)
   Raid Devices : 2
  Total Devices : 2
    Persistence : Superblock is persistent

    Update Time : Sat Dec  8 11:39:47 2018
          State : clean 
 Active Devices : 2
Working Devices : 2
 Failed Devices : 0
  Spare Devices : 0

     Chunk Size : 512K

           Name : he2:2  (local to host he2)
           UUID : b1343f78:6b8d1f99:211f073d:323d1683
         Events : 0

    Number   Major   Minor   RaidDevice State
       0       8        7        0      active sync   /dev/sda7
       1       8       23        1      active sync   /dev/sdb7

/Martin


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#16 2019-09-08 14:31:17

Martin
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From: Stockholm, Sweden
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Re: Accidentally re-formatted boot sector :-(

rbh wrote:
Martin wrote:

md0 (now back to ext4 from a temporary fat32 life):

I missed this before. Did you convert fat32>ext4 now after your missfortune?
Why did you convert it? The size and partitiontype hints that it is an uefi-partion. UEFI partition must be in fat to support booting.

What I intended to to late on Friday was to re-format a pen-drive. Hence fat32. Too late it struck me as rather odd that said pen-drive was ext4 just before re-formatting. The rest is history... Don't do these kind of things late on Friday after a looong work week...

rbh wrote:

If you have the time to spare, you can try to fix your missfortune, else it might be better to reinstall.

You can install Helium and upgrade to buster/lithium-dev.

I hoped to find a way back involving less work than re-installing Helium. This is my primary machine so going for Lithium alpha or even beta is not really what I would like to do. That is for virtual machines or my tertiary machine.

/Martin


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#17 2019-09-08 20:51:55

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 351
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Re: Accidentally re-formatted boot sector :-(

eight.bit.al wrote:

Does the UUID in fstab match the UUID of the actual partition?
And so forth...

Just checked this and found disagrement. I edited fstab and md0 promptly disapeared from Thunar. Checking with GParted I now find it has the mount point /boot (missing in the screen shot above). lsblk does not see this mount point though:

martin@he2:~$ lsblk -f
NAME    FSTYPE         LABEL       UUID                                 MOUNTPOINT
sda                                                                     
├─sda1  linux_raid_mem he2:0       f8d3a77f-8a8d-c09e-2535-1387b1a0d42d 
│ └─md0 ext4                       4666049c-8f1e-4f0d-89bc-10d8e14a5a6c 
├─sda2  linux_raid_mem he2:1       4bcd4789-cb0b-b8f2-ba5a-47f71e3e0cd8 
│ └─md1 swap                       89c3dd1a-ed27-4b77-8c29-a2cc9e599a96 [SWAP]
├─sda5  btrfs                      d112bfbd-53ca-4d8e-a8a9-f7a4b5d15f52 /
├─sda6  btrfs                      84136c02-e53e-43f6-b5d2-85999816add0 /home
└─sda7  linux_raid_mem he2:2       b1343f78-6b8d-1f99-211f-073d323d1683 
  └─md2 ext4                       f0210d74-89ad-46c8-ba11-c91b9245bedd /extra
sdb                                                                     
├─sdb1  linux_raid_mem he2:0       f8d3a77f-8a8d-c09e-2535-1387b1a0d42d 
│ └─md0 ext4                       4666049c-8f1e-4f0d-89bc-10d8e14a5a6c 
├─sdb2  linux_raid_mem he2:1       4bcd4789-cb0b-b8f2-ba5a-47f71e3e0cd8 
│ └─md1 swap                       89c3dd1a-ed27-4b77-8c29-a2cc9e599a96 [SWAP]
├─sdb5  btrfs                      d112bfbd-53ca-4d8e-a8a9-f7a4b5d15f52 
├─sdb6  btrfs                      84136c02-e53e-43f6-b5d2-85999816add0 
└─sdb7  linux_raid_mem he2:2       b1343f78-6b8d-1f99-211f-073d323d1683 
  └─md2 ext4                       f0210d74-89ad-46c8-ba11-c91b9245bedd /extra
sdc     vfat           SANSA CLIPP 10C8-FCE4                            /media/martin/SANSA CL
sr0 

/Martin

Last edited by Martin (2019-09-08 20:56:00)


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#18 2019-09-09 10:04:00

rbh
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From: Sweden/Vasterbotten/Rusfors
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Posts: 60

Re: Accidentally re-formatted boot sector :-(

Lets sort out all contradictory information:

You hawe formated md0 (sda1-sdb1, raid1) /boot.
In december it was not mounted either..

/boot will be populated again when you reinstall grubb.
(200 mb is small, with disks of today. If you reinstall, set at least 500 mb aside for /boot. Btw, I prefer ext2 on /boot. No need for journaling FS on /boot...)

Md0 is healthy.

Md1 swap (sda1-sdb1 raid0) - healthy

Mdx (sda5-sdb5) / - missing
Only sda5 mounted on /
What does your /etc/mdadm/mdadm.conf says?

Mdx has to be reasembled.

Mdxx (sda6-sdb6) /home - missing
Only sda6 mounted on /home
Mdxx has to be reasembled.

Md2 (sda7-sdb7 raid0!) /extra - healty
Whith raid0, all information is lost if one in the raidgroup gets lost. Good for perfomrance, bad for redundancy... You are aware of that you have mixed raid9 and raid1?

I would ensure that partion on sda5 and sda6 is healthy before reasembling.
First backup essential data, then reboot on an rescue-cd.

If you are not familiar with raid management, it probably means more work than reinstalling BL Helium...

Installing BL-helium and uppgrade Debian to Buster, is safe.
You can choose to stay with Helium until official release of lithium. But, Lithium-dev, is not unstable...

Last edited by rbh (2019-09-09 10:06:23)


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#19 2019-09-09 12:15:23

eight.bit.al
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Posts: 294
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Re: Accidentally re-formatted boot sector :-(

rbh wrote:

You are aware of that you have mixed raid9 and raid1?

Emphasis mine.
Following your good advice with interest. Is that a typo, you meant raid0?
Thanks for helping with Martin"s missfortune.

8bit

yikes

Last edited by eight.bit.al (2019-09-09 12:19:39)

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#20 2019-09-09 16:11:57

rbh
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From: Sweden/Vasterbotten/Rusfors
Registered: 2016-08-11
Posts: 60

Re: Accidentally re-formatted boot sector :-(

eight.bit.al wrote:
rbh wrote:

You are aware of that you have mixed raid9 and raid1?

Is that a typo, you meant raid0?
yikes

Yes! Fat fingers and old, tired eyes. Did not catch that typo...


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#21 2019-09-09 18:46:19

Martin
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From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 351
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Re: Accidentally re-formatted boot sector :-(

Thanks for the effort! Very enlightening.
Comments and attempted answers/explanations inserted below.

rbh wrote:

Lets sort out all contradictory information:

You hawe formated md0 (sda1-sdb1, raid1) /boot.
In december it was not mounted either..

/boot will be populated again when you reinstall grubb.
(200 mb is small, with disks of today. If you reinstall, set at least 500 mb aside for /boot. Btw, I prefer ext2 on /boot. No need for journaling FS on /boot...)

Md0 is healthy.

Good. I will try re-installing Grub later. Is there any drawback with ext4 for /boot? (I don't remember why I did this choice.)

rbh wrote:

Md1 swap (sda1-sdb1 raid0) - healthy

Good.

rbh wrote:

Mdx (sda5-sdb5) / - missing
Only sda5 mounted on /
What does your /etc/mdadm/mdadm.conf says?

Mdx has to be reasembled.

Mdxx (sda6-sdb6) /home - missing
Only sda6 mounted on /home
Mdxx has to be reasembled.

Raiding is governed by btrfs for these.

rbh wrote:

Md2 (sda7-sdb7 raid0!) /extra - healty
Whith raid0, all information is lost if one in the raidgroup gets lost. Good for perfomrance, bad for redundancy... You are aware of that you have mixed raid9 and raid1?

I use redundancy for /boot and where I store user data and go for speed elsewhere.

rbh wrote:

I would ensure that partion on sda5 and sda6 is healthy before reasembling.
First backup essential data, then reboot on an rescue-cd.

So installing Grub from the still running system to get Grub installed does not work (see a previous post)? It is only possible from the 'outside' using a rescue-cd?

rbh wrote:

If you are not familiar with raid management, it probably means more work than reinstalling BL Helium...

Installing BL-helium and uppgrade Debian to Buster, is safe.
You can choose to stay with Helium until official release of lithium. But, Lithium-dev, is not unstable...

Very tempting. There are one or two updates available in Buster I'd rather get access to.

/Martin


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prove their worth by hitting back."
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#22 2019-09-10 11:09:39

rbh
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From: Sweden/Vasterbotten/Rusfors
Registered: 2016-08-11
Posts: 60

Re: Accidentally re-formatted boot sector :-(

Martin wrote:

Good. I will try re-installing Grub later. Is there any drawback with ext4 for /boot? (I don't remember why I did this choice.)

Ext3/4 is journaling filesystem. There is not much writing to /boot, hence no need for journal.

Martin wrote:

Raiding is governed by btrfs for these.

So I've learned someting new again. Sofar I've onlu used btrfs for ReactOS installation. Maybe time to look closer att it.

Martin wrote:

So installing Grub from the still running system to get Grub installed does not work (see a previous post)? It is only possible from the 'outside' using a rescue-cd?

No. Only fsck, require to boot on rescue-disk. If your btrfs-raid is heathy, no need to reboot.
But!... maybe you will run inte trouble installing grubb to raided partition.

When I installed my server for a couple of years, i did not raided boot. Now, i thougt it would be time to do it. When I added the boot partion to an raid, i ended up with an empty ext2 fs. When i reinstalled grub, I got an error, saying that ext2, does not support embedding. Same error message when i formated to ext3 or ext4..
No problem reinstall grubb when i broke up the raid for /boot.

Let us know how you manage.


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// Regards rbh

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#23 2019-09-11 20:18:15

Martin
Member
From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 351
Website

Re: Accidentally re-formatted boot sector :-(

I tried installing grub from command line. No error messages but re-booting did not go well so I decided to re-install Helium. I now have a very bare-bones Helium install and will try upgrading to Debian 10 before I invest any time in re-creating my set-up and program favourites installation.

/Martin


"Problems worthy of attack
prove their worth by hitting back."
Piet Hein

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#24 2019-09-12 06:33:35

Martin
Member
From: Stockholm, Sweden
Registered: 2015-10-01
Posts: 351
Website

Re: Accidentally re-formatted boot sector :-(

First post from new install.

bl-welcome did not work blaming dated signatures for BL repos.

Running Buster now AFAIK. That up-grade process was smooth.
Still a lot of work remaining to install my favorites and setting them up.

/Martin


"Problems worthy of attack
prove their worth by hitting back."
Piet Hein

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#25 2019-09-12 07:43:03

rbh
Member
From: Sweden/Vasterbotten/Rusfors
Registered: 2016-08-11
Posts: 60

Re: Accidentally re-formatted boot sector :-(

Martin wrote:

bl-welcome did not work blaming dated signatures for BL repos.

I suppose you used old isos? Not the latest helium-5-... updated in july?

You can download and install latest bunsenkeyring

# wget https://eu.pkg.bunsenlabs.org/debian/po … -2_all.deb
# dpkg -i bunsen-keyring_2019.01.19+bl9-2_all.deb

Then you can update andupgrade helium packages.

Martin wrote:

Still a lot of work remaining to install my favorites and setting them up.

It is possible from rescue-mode or rescue-cd export list of all installed packages and then import that after reinstalling.

On the other hand, its not bad to clean out...

Last edited by rbh (2019-09-12 07:45:00)


God readings: FORUM RULES and Help page for forum post formatting

// Regards rbh

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