Missing drives & mismatched tables (MBR vs GPT)

idee · April 11, 2024, 11:42pm

I was testing distros (Lubuntu & Bodhi) via live usb drive, liked what I saw and installed them on a couple of test partitions. I messed something up bad. I booted into Lubuntu grub, but nothing would start. I had to install a 15.5 upgrade (from 15.4) to clean up openSuSE and let it take over. It installed, but only started in emergency mode. Looking through the logs I found that multiple partitions were not loading. The solution was to edit fstab using Vi to rem out the missing partitions. Once the system was running I saw that 2 of 4 drives are missing. During a reboot, the bios also shows 2 missing drives. One of the reboots I noticed text before Grub that mentioned mismatched tables.

Before the update to 15.5, when I was trying to “fix” things with Gparted, it showed all 4 drives with all partitions visible. I have not rebooted to Gparted-live yet to see what it shows currently.

Is there an openSuSE rescue disk (like previously) available that can clean out the MBR and grub? I think due to not understanding the Ubuntu installers I mixed MBR and GPT.

Below is some information on the system. Thank you in advance for any help. Please let me know anything more you need to help.

dad@localhost:~> sudo fdisk -l /dev/sda

Disk /dev/sda: 111.79 GiB, 120034123776 bytes, 234441648 sectors
Disk model: CT120BX100SSD1  
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x000e061b

Device     Boot     Start       End   Sectors  Size Id Type
/dev/sda1  *         2048  52430847  52428800   25G 83 Linux
/dev/sda2        52430848 104859647  52428800   25G 83 Linux
/dev/sda3       104859648 119539711  14680064    7G 82 Linux swap / Solaris
/dev/sda4       119541758 233406463 113864706 54.3G  f W95 Ext'd (LBA)
/dev/sda5       176166912 232790015  56623104   27G 83 Linux
/dev/sda6       232792064 233406463    614400  300M ef EFI (FAT-12/16/32)
/dev/sda7       119543808 176164863  56621056   27G 83 Linux

Partition table entries are not in disk order.

dad@localhost:~> sudo fdisk -l /dev/sdb
Disk /dev/sdb: 465.76 GiB, 500107862016 bytes, 976773168 sectors
Disk model: Samsung SSD 870 
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt          
Disk identifier: 68A1BE66-D900-434E-AE28-C19BB8F3815D
                                           
Device         Start       End   Sectors  Size Type 
/dev/sdb1       2048 629147647 629145600  300G Linux filesystem  
/dev/sdb2  629147648 975177727 346030080  165G Linux filesystem      
/dev/sdb3  975177728 976773119   1595392  779M Linux filesystem   
           
dad@localhost:~> sudo fdisk -l /dev/sdc
fdisk: cannot open /dev/sdc: No such file or directory 
                               
dad@localhost:~> sudo fdisk -l /dev/sdd
fdisk: cannot open /dev/sdd: No such file or directory

Information provided via TestDisk

Christophe GRENIER <grenier@cgsecurity.org>                                                                  
https://www.cgsecurity.org                                                                                   
                                                                                                             
 - - selected Intel/PC partition – testdisk noted that was detected - - 

Disk /dev/sda - 120 GB / 111 GiB - CHS 14593 255 63 

Hint: Intel partition table type has been detected.                                              
Note: Do NOT select 'None' for media with only a single partition. It's very                     
rare for a disk to be 'Non-partitioned'. 
                                                         
Current partition structure:                                                                                 
     Partition                  Start        End    Size in sectors                                          
                                                                                                             
 1 * Linux                    0  32 33  3263 170 43   52428800 [LXQT-root]                                   
Bad relative sector.                                                                                         
 2 P Linux                 3263 170 44  6527  53 54   52428800 [LXQT-home]                                   
 3 P Linux Swap            6527  53 55  7441   0 47   14680064                                               
 4 E extended LBA          7441  33 15 14528 224 32  113864706                                               
 5 L Linux                10965 225 13 14490 129 39   56623104 [/U-home]                                     
   X extended             14490 161 58 14528 224 32     614414                                               
 6 L EFI (FAT-12/16/32)   14490 162  9 14528 224 32     614400                                               
   X extended              7441  60 46 10965 192 43   56621374                                               
 7 L Linux                 7441  65 49 10965 192 43   56621056 [Lubuntu]  

----------------------------------------------------------

TestDisk 7.1, Data Recovery Utility, July 2019                                                               
Christophe GRENIER <grenier@cgsecurity.org>                                                                  
https://www.cgsecurity.org                                                                                   
 
 - - selected GPT partition – since the problems noted mismatched tables - - 
                                                                                                            
Disk /dev/sda - 120 GB / 111 GiB - CHS 14593 255 63                                                          
Current partition structure:                                                                                 
     Partition                  Start        End    Size in sectors                                          
                                                                                                             
Bad GPT partition, invalid signature.                                                                        
Trying alternate GPT                                                                                         
Bad GPT partition, invalid signature.                                                                        
 
----------------------------------------------------------

Disk /dev/sda - 120 GB / 111 GiB - CHS 14593 255 63                                                          
     Partition               Start        End    Size in sectors                                             
 P Linux filesys. data         2048   52430847   52428800 [LXQT-root]                                        
 P Linux filesys. data     52430848  104859647   52428800 [LXQT-home]                                        
 P Linux Swap             104859648  119539695   14680048                                                    
 P Linux filesys. data    119543808  176164863   56621056 [Lubuntu]                                          
 P Linux filesys. data    176166912  232790015   56623104 [/U-home]                                          
 P EFI System             232792064  233406439     614376 [EFI System Partition] [boot-efi] 
  
----------------------------------------------------------
----------------------------------------------------------
Disk /dev/sdb - 500 GB / 465 GiB - Samsung SSD 870 EVO 500GB 

Hint: EFI GPT partition table type has been detected.                                                        
Note: Do NOT select 'None' for media with only a single partition. It's very                                 
rare for a disk to be 'Non-partitioned'. 

Current partition structure:                                                                                 
     Partition                  Start        End    Size in sectors                                          
                                                                                                             
 1 P Linux filesys. data         2048  629147647  629145600                                                  
 2 P Linux filesys. data    629147648  975177727  346030080                                                  
 3 P Linux filesys. data    975177728  976773119    1595392 

----------------------------------------------------------
                                     
 Disk /dev/sdb - 500 GB / 465 GiB - CHS 60801 255 63                                                          
                                                                                                             
     Partition                  Start        End    Size in sectors                                          
                                                                                                             
  Linux filesys. data         2048  629147647  629145600 [data1]                                             
superblock 0, blocksize=4096 [data1]                                                                         
superblock 32768, blocksize=4096 [data1]                                                                     
superblock 98304, blocksize=4096 [data1]                                                                     
superblock 163840, blocksize=4096 [data1]                                                                    
superblock 229376, blocksize=4096 [data1]                                                                    
superblock 294912, blocksize=4096 [data1]                                                                    
superblock 819200, blocksize=4096 [data1]                                                                    
superblock 884736, blocksize=4096 [data1]                                                                    
superblock 1605632, blocksize=4096 [data1]                                                                   
superblock 2654208, blocksize=4096 [data1]                                                                   
                                                                                                             
To repair the filesystem using alternate superblock, run                                                     
fsck.ext4 -p -b superblock -B blocksize device                              

----------------------------------------------------------
Disk /dev/sdb - 500 GB / 465 GiB - CHS 60801 255 63 

-- selected Intel/PC as a test --
                                             
Current partition structure:                                                                     
     Partition                  Start        End    Size in sectors                              
                                                                                                 
 1 P EFI GPT                  0   0  2 60801  80 63  976773167                                   
                                                                                                 
Warning: Bad ending head (CHS and LBA don't match)                                               
No partition is bootable 
                                     
----------------------------------------------------------
 
dad@localhost:~> sudo testdisk /list
TestDisk 7.1, Data Recovery Utility, July 2019                                                   
Christophe GRENIER <grenier@cgsecurity.org>                                                    
https://www.cgsecurity.org
Please wait...
Disk /dev/sda - 120 GB / 111 GiB - CHS 14593 255 63
Sector size:512
Model: CT120BX100SSD1, S/N:1527F009453E, FW:MU02

Disk /dev/sdb - 500 GB / 465 GiB - CHS 60801 255 63
Sector size:512
Model: Samsung SSD 870 EVO 500GB, S/N:S62ANJ0R400091L, FW:SVT01B6Q

Disk /dev/sda - 120 GB / 111 GiB - CHS 14593 255 63
     Partition                  Start        End    Size in sectors
 1 * Linux                    0  32 33  3263 170 43   52428800 [LXQT-root]
     btrfs blocksize=4096 Backup superblock
 2 P Linux                 3263 170 44  6527  53 54   52428800 [LXQT-home]
     ext4 blocksize=4096 Large_file Sparse_SB Recover
 3 P Linux Swap            6527  53 55  7441   0 47   14680064
     SWAP2 version 1, pagesize=4096
 4 E extended LBA          7441  33 15 14528 224 32  113864706
   X extended              7441  60 46 10965 192 43   56621374
 7 L Linux                 7441  65 49 10965 192 43   56621056 [Lubuntu]
     btrfs blocksize=4096 Backup superblock
 5 L Linux                10965 225 13 14490 129 39   56623104 [/U-home]
     ext4 blocksize=4096 Large_file Sparse_SB
   X extended             14490 161 58 14528 224 32     614414
 6 L EFI (FAT-12/16/32)   14490 162  9 14528 224 32     614400

Disk /dev/sdb - 500 GB / 465 GiB - CHS 60801 255 63
     Partition                  Start        End    Size in sectors
 1 P Linux filesys. data         2048  629147647  629145600
 2 P Linux filesys. data    629147648  975177727  346030080
 3 P Linux filesys. data    975177728  976773119    1595392

OpenSuSE 15.5 - LXQT

idee · April 12, 2024, 12:05am

I found this while researching the mismatched tables issue.

FixParts
https://www.rodsbooks.com/fixparts/

From that page: “It can remove stray GUID Partition Table (GPT) data, …”

Also the following that I am still reading,

arvidjaar · April 12, 2024, 4:20am

If drives are missing in BIOS already, it has nothing to do with operating system. It is some hardware issue.

idee · April 12, 2024, 5:37am

After multiple boots and working through the bios settings it seems to have cleared up. All 4 drives are now available. I can’t take any credit, it seems to be a function of it doing something through the multiple boots. At one point there were 3, and then after a couple more reboots there were 4. It also sped up from dog slow, to back to normal fast.

I still see the mismatched note fly by before grub, but I have not been able to capture it yet either as a pause, or in a picture. Is there anything I could check for that? Is it possible that may still be a conflict in there somewhere?

dcurtisfra · April 12, 2024, 9:46am

Or, the BIOS either needs to be updated or, it’s corrupt …

Yet another reason to only use UEFI/BIOS which can be updated from within the BIOS/UEFI itself …
Without needing an Operating System which provides a Utility to update/over-write the BIOS/UEFI …

dcurtisfra · April 12, 2024, 9:48am

@idee:

> lsblk --fs

– is a reliable method to determine which drives an partitions are currently recognised by the Linux Kernel …

idee · April 12, 2024, 2:20pm

Thanks for the help.

Update, the 4 drives are now in the bios tool and it starts clean as opposed to super slow like it was, but partition tool only sees 3. sdd is still missing.

Here is that output:

dad@puppypc6481:~> lsblk --fs
NAME FSTYPE FSVER LABEL UUID                                 FSAVAIL FSUSE% MOUNTPOINTS
sda                                                                         
├─sda1
│    btrfs        backups
│                       d5671095-81d9-4fa6-9eec-fec09fa68b9a    1.5T    14% /backups
└─sda2
     vfat   FAT32 shared
                        4814-2CF7                             122.2G     0% /fat-shared
sdb                                                                         
├─sdb1
│    btrfs        LXQT-root
│                       41b2639a-9e6f-4c29-8c31-834ff320c7f7   10.5G    57% /var
│                                                                           /usr/local
│                                                                           /tmp
│                                                                           /opt
│                                                                           /boot/grub2/x86_64-efi
│                                                                           /root
│                                                                           /srv
│                                                                           /boot/grub2/i386-pc
│                                                                           /
├─sdb2
│    ext4   1.0   LXQT-home
│                       d511d672-ec38-4611-8c19-a518e8471d66   12.5G    44% /home
├─sdb3
│    swap   1           4571b93d-b13a-4a68-8a27-ea8ee6707aff                [SWAP]
├─sdb4
│                                                                           
├─sdb5
│    ext4   1.0   U-home
│                       2ad2a48c-39e7-44ca-bc65-0bc6bff4f47c     25G     0% /U-home
├─sdb6
│    vfat   FAT16 boot-efi
│                       8B7B-8BF0                             293.7M     2% /boot/efi
└─sdb7
     btrfs        Lubuntu
                        e5e42368-dc6f-41c1-8a2f-3e7a334efc1f   26.5G     0% /Lubuntu
sdc                                                                         
├─sdc1
│    ext4   1.0   data1 32dec515-60ad-4718-96ad-ad50408d1919  117.4G    55% /data1
├─sdc2
│    ext4   1.0   data2 2e2c7db7-8441-4ef4-9d81-3b1b57d671f9   77.8G    47% /data2
└─sdc3
     ext4   1.0   test760
                        3cd0b56e-9597-4cfc-854a-4646fb8cd8b8  694.7M     0% /test
sr0                                                                         
dad@puppypc6481:~> lsblk --fs
NAME   FSTYPE FSVER LABEL     UUID                                 FSAVAIL FSUSE% MOUNTPOINTS
sda                                                                                                
├─sda1 btrfs        backups   d5671095-81d9-4fa6-9eec-fec09fa68b9a    1.5T    14% /backups              
└─sda2 vfat   FAT32 shared    4814-2CF7                             122.2G     0% /fat-shared              
sdb                                                                                                         
├─sdb1 btrfs        LXQT-root 41b2639a-9e6f-4c29-8c31-834ff320c7f7   10.5G    57% /var                                    
│                                                                                 /usr/local                                
│                                                                                 /tmp
│                                                                                 /opt
│                                                                                 /boot/grub2/x86_64-efi
│                                                                                 /root
│                                                                                 /srv
│                                                                                 /boot/grub2/i386-pc
│                                                                                 /
├─sdb2 ext4   1.0   LXQT-home d511d672-ec38-4611-8c19-a518e8471d66   12.5G    44% /home
├─sdb3 swap   1               4571b93d-b13a-4a68-8a27-ea8ee6707aff                [SWAP]
├─sdb4                                                                            
├─sdb5 ext4   1.0   U-home    2ad2a48c-39e7-44ca-bc65-0bc6bff4f47c     25G     0% /U-home
├─sdb6 vfat   FAT16 boot-efi  8B7B-8BF0                             293.7M     2% /boot/efi
└─sdb7 btrfs        Lubuntu   e5e42368-dc6f-41c1-8a2f-3e7a334efc1f   26.5G     0% /Lubuntu
sdc                                                                               
├─sdc1 ext4   1.0   data1     32dec515-60ad-4718-96ad-ad50408d1919  117.4G    55% /data1
├─sdc2 ext4   1.0   data2     2e2c7db7-8441-4ef4-9d81-3b1b57d671f9   77.8G    47% /data2
└─sdc3 ext4   1.0   test760   3cd0b56e-9597-4cfc-854a-4646fb8cd8b8  694.7M     0% /test
sr0

A very strange thing just happened. The pc has changed names. Which isn’t possible, but don’t know what happened. I am aware of puppy linux, but have never used it. How do I change that? How was it changed? The only thing I can think of is that I started to look at setting up a lan last night, but didn’t make any changes yet.

yesterday was (see initial post above):
dad@localhost:~>

this morning is:
dad@puppypc6481:~>

idee · April 13, 2024, 12:43am

For the UEFI/BIOS, that is pretty much determined by the motherboard isn’t it? Is there anything that can be done with that? If so, I’d be glad to hear it.

The initial request for help is how to check the MBR for any errors or mismatches, and if identified, how to make the corrections. Anything I can do?

The testdisk app. provided a diagnostic report. What is the method to upload a file into the forum. I remember there being a way, but not how to do it.

thanks,

idee · April 13, 2024, 8:27pm

Is anyone familiar with how to check the MBR for any errors or mismatches, and if identified, how to make the corrections.

malcolmlewis · April 13, 2024, 9:07pm

@idee The hostname is likely coming from your router and your using dhcp to get your IP address. The test disk probably uses puppylinux perhaps? You should set your hostname proper with hostnamectl command?

So can you show a picture of the BIOS and the devices present? The missing device what type of storage device is it? Sure it’s not cabling or power (5V and 12V) to the missing device?

idee · April 13, 2024, 9:48pm

Thank you Malcolm,
The hostnamectl returned the following. I’ll reset it. I have never used puppy, so that is strange. Loaded a live disk a couple of weeks ago.

hostnamectl
   Static hostname: n/a                                   
Transient hostname: puppypc6481
         Icon name: computer-desktop
           Chassis: desktop
        Machine ID: 0fe395f5367a4688acaa31c7f9f68449
           Boot ID: 28696925e2624cea875526b1ec33fcc5
  Operating System: openSUSE Leap 15.5                    
       CPE OS Name: cpe:/o:opensuse:leap:15.5
            Kernel: Linux 5.14.21-150500.55.52-default
      Architecture: x86-64
   Hardware Vendor: Hewlett-Packard
    Hardware Model: HP Compaq dc7900 Convertible Minitower

I am trying to set up a lan between a couple of computers and am reading through that now. Is there a basics tutorial you might recommend? I am not so sure I need Samba, was going to go old school. I only use windows once a year at tax season.

I will reboot and get a picture of the bios and send it soon.

Here is a screenshot from partitioner

Here is last year. Same hardware. SDD is what is missing currently

type or paste code here

malcolmlewis · April 13, 2024, 11:47pm

@idee so run hostnamectl set-hostname <your_hostname> to set…

When was the last time you saw the device visible on an OS? Suggest you check (maybe replace) cables and check power supply.

idee · April 14, 2024, 3:08am

Everything was working fine until I ran a live disk of Lubuntu and then installed it in a test partition. I believe I made a poor selection and may have corrupted the MBR. There was a recommendation for Linux to use GPT, which I didn’t realize might conflict with my existing system. That was when the problems started, just a couple of days ago.

Below are pictures of the bios. It was doing strange things, changing from 2 sata devices to 3 sata devices, back and forth and not allowing the reboot. Finally it took, and completed the boot process.

Sometimes it would stall at the bios screen until F9 or F10 were selected. That is when it was bouncing between 2 or 3 sata devices.

I will be checking the cables and removing those two (sdc and sdd) in a few minutes.

malcolmlewis · April 14, 2024, 3:20am

@idee you shouldn’t need the boot agent for PXE boot? Sure it hasn’t changed to some sort of RAID/JBOD setup or not using AHCI?

What does it show under Storage Options?

idee · April 14, 2024, 4:05am

Malcolm,
Other that boot order I have not made changes in the bios.
PXE?
Not sure about RAID/JBOD setup or not using AHCI changes. I haven’t knowingly made any changes.

What should I look at? or is there a command prompt?
I will reboot for the Storage Options.

idee · April 15, 2024, 2:19am

Here are some other bios screens

idee · April 15, 2024, 4:02am

It may have been a coincidence of a hard drive going out at the same time as I was testing the live distros. I removed the 4th drive that had been missing in the bios. Everything cleaned up and sped up. The oddity of also having the 3rd drive pop in and out I will keep an eye on. I am running a diagnostic test on it now. For now, that seems to have been the culprit. I will jump back in if it starts having issues again.

Here is the DisKMonitor for sdc

Thanks for the help Malcolm.

Last question on the networking tutorial, any suggestions.

system · April 29, 2024, 12:49pm

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