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Thread: RAID woes, can't repartition my hard drives

  1. #1
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    RAID woes, can't repartition my hard drives

    Hi folks,

    A little bird told me that the Server forums would be the best place to seek advice on RAID. I've just tried to delete the partitions on a system that had (and maybe still has vestiges of) a RAID1, built with mdadm and the old MS-DOS MBR. I thought I had a perfect configuration to install Ubuntu 13.04 along-side 12.04, but my installation attempts have aborted at the grub-install step.

    It was suggested that I upgrade from MBR to gpt, or LVM. I don't actually need more than four physical partitions on each hard drive, an amount which MBR can handle. But something was standing in the way of my installation process. From some of the prompts I was getting when trying to install 13.04, I felt like I was getting hints to use logical, rather than physical, volume management.

    I backed up my /home directory to an external drive, booted from the 13.04 live disk, installed mdadm, attempted to disassemble the RAID, and then reformat the hard drives. I'm stuck. I can't seem to create a new partition table. GParted complains thus: "Partition(s) 2 on /dev/sda have been written, but we have been unable to inform the kernel of the change, probably because it/they are in use. As a result, the old partition(s) will remain in use. You should reboot now before making further changes." I have gotten similar messages when I try to create partitions: the system claims that I'm using partitions that I have only just created.

    I found some rather dated instructions for killing an old RAID setup, once and for all. I followed these steps, but they aren't working for me.

    Thanks for any help you can provide!

  2. #2
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    Re: RAID woes, can't repartition my hard drives

    1. Make sure you are not mounting any partitions!
    2. Make sure you unmount any swap partition that might exist on the disk if you are doing this from live mode, because swap gets mounted in live mode automatically to speed it up!

    There is no special procedure for deleting mdadm setup/partitions, especially if you plan to write new partition table on the disk anyway. If you want to use existing partition that was part of mdadm array, you need to zero the superblock first, so that it will be considered as a brand new partition never used in mdadm.
    But creating new partition table removes all partitions with their superblocks anyway, so this step is not needed.

    From live mode can you post the output of:
    Code:
    cat /proc/mdstat
    sudo parted -l
    df -h
    Darko.
    -----------------------------------------------------------------------
    Ubuntu 12.04 LTS 64bit & Windows 7 Ultimate 64bit

  3. #3
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    Re: RAID woes, can't repartition my hard drives

    Thank you darkod, here is the output you requested -- plus, the output of the mount command:

    Code:
    ubuntu@ubuntu:~$ cat /proc/mdstat
    
    Personalities : [raid1] 
    md127 : inactive sda2[0](S)
          20955136 blocks super 1.2
           
    unused devices: <none>
    
    
    
    ubuntu@ubuntu:~$ sudo parted -l
    
    Model: ATA WDC WD6401AALS-0 (scsi)
    Disk /dev/sda: 640GB
    Sector size (logical/physical): 512B/512B
    Partition Table: gpt
    
    Number  Start  End  Size  File system  Name  Flags
    
    
    Model: ATA WDC WD7501AALS-0 (scsi)
    Disk /dev/sdb: 750GB
    Sector size (logical/physical): 512B/512B
    Partition Table: gpt
    
    Number  Start  End  Size  File system  Name  Flags
    
    
    Warning: Unable to open /dev/sr0 read-write (Read-only file system).  /dev/sr0
    has been opened read-only.
    Error: Can't have a partition outside the disk!                           
    
    
    
    ubuntu@ubuntu:~$ df -h
    
    Filesystem      Size  Used Avail Use% Mounted on
    /cow            3.9G  499M  3.5G  13% /
    udev            3.9G   12K  3.9G   1% /dev
    tmpfs           799M  900K  798M   1% /run
    /dev/sr0        785M  785M     0 100% /cdrom
    /dev/loop0      738M  738M     0 100% /rofs
    none            4.0K     0  4.0K   0% /sys/fs/cgroup
    tmpfs           3.9G  1.2M  3.9G   1% /tmp
    none            5.0M     0  5.0M   0% /run/lock
    none            3.9G  148K  3.9G   1% /run/shm
    none            100M   48K  100M   1% /run/user
    
    
    
    ubuntu@ubuntu:~$ mount
    
    /cow on / type overlayfs (rw)
    proc on /proc type proc (rw,noexec,nosuid,nodev)
    sysfs on /sys type sysfs (rw,noexec,nosuid,nodev)
    udev on /dev type devtmpfs (rw,mode=0755)
    devpts on /dev/pts type devpts (rw,noexec,nosuid,gid=5,mode=0620)
    tmpfs on /run type tmpfs (rw,noexec,nosuid,size=10%,mode=0755)
    /dev/sr0 on /cdrom type iso9660 (ro,noatime)
    /dev/loop0 on /rofs type squashfs (ro,noatime)
    none on /sys/fs/cgroup type tmpfs (rw)
    none on /sys/fs/fuse/connections type fusectl (rw)
    none on /sys/kernel/debug type debugfs (rw)
    none on /sys/kernel/security type securityfs (rw)
    tmpfs on /tmp type tmpfs (rw,nosuid,nodev)
    none on /run/lock type tmpfs (rw,noexec,nosuid,nodev,size=5242880)
    none on /run/shm type tmpfs (rw,nosuid,nodev)
    none on /run/user type tmpfs (rw,noexec,nosuid,nodev,size=104857600,mode=0755)
    gvfsd-fuse on /run/user/ubuntu/gvfs type fuse.gvfsd-fuse (rw,nosuid,nodev,user=ubuntu)
    I am leaving this system turned on until I resolve the problem. I don't want things to get changed by a reboot.
    Last edited by ladasky; June 12th, 2013 at 07:12 PM.

  4. #4
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    Re: RAID woes, can't repartition my hard drives

    Have you tried something like:
    Code:
    sudo mdadm --stop /dev/md127
    sudo mdadm --zero-superblock /dev/sda2
    Then open /etc/mdadm/mdadm.conf and remove all ARRAY definitions that might be there. Save and close the file.

    That should be it. You can try making partitions on the disks with or without rebooting.
    Darko.
    -----------------------------------------------------------------------
    Ubuntu 12.04 LTS 64bit & Windows 7 Ultimate 64bit

  5. #5
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    Re: RAID woes, can't repartition my hard drives

    Thanks again, darkod, for your continued help.

    Quote Originally Posted by darkod View Post
    Have you tried something like:
    Code:
    sudo mdadm --stop /dev/md127
    sudo mdadm --zero-superblock /dev/sda2
    I have done things like this before, but I just did it again. I keep getting stray logical partitions made, which I then have to remove, when GParted does the job half-way.

    Quote Originally Posted by darkod View Post
    Then open /etc/mdadm/mdadm.conf and remove all ARRAY definitions that might be there. Save and close the file.
    My mdadm.conf had no array definitions, so I didn't edit it.

    Code:
    # mdadm.conf
    #
    # Please refer to mdadm.conf(5) for information about this file.
    #
    
    # by default (built-in), scan all partitions (/proc/partitions) and all
    # containers for MD superblocks. alternatively, specify devices to scan, using
    # wildcards if desired.
    #DEVICE partitions containers
    
    # auto-create devices with Debian standard permissions
    CREATE owner=root group=disk mode=0660 auto=yes
    
    # automatically tag new arrays as belonging to the local system
    HOMEHOST <system>
    
    # instruct the monitoring daemon where to send mail alerts
    MAILADDR root
    
    # definitions of existing MD arrays
    
    # This file was auto-generated on Wed, 12 Jun 2013 07:51:31 +0000
    # by mkconf $Id$
    Quote Originally Posted by darkod View Post
    That should be it. You can try making partitions on the disks with or without rebooting.
    Ah well, I made some progress, but I'm still not all the way there. I got all the way through /dev/sda this time, but then I got a mkfs error on /dev/sdb. The computer claims that /dev/sdb1 is in use. I have seen this kind of error several times. Here is the error output from gparted_details.htm:

    Code:
    GParted 0.12.1 --enable-libparted-dmraid
    
    Libparted 2.3
    Create Primary Partition #1 (ext4, 30.00 GiB) on /dev/sda  00:00:02    ( SUCCESS )
         	
    create empty partition  00:00:00    ( SUCCESS )
         	
    path: /dev/sda1
    start: 2,048
    end: 62,916,607
    size: 62,914,560 (30.00 GiB)
    set partition type on /dev/sda1  00:00:00    ( SUCCESS )
         	
    new partition type: ext4
    create new ext4 file system  00:00:02    ( SUCCESS )
         	
    mkfs.ext4 -j -O extent -L "OS1a" /dev/sda1
         	
    Filesystem label=OS1a
    OS type: Linux
    Block size=4096 (log=2)
    Fragment size=4096 (log=2)
    Stride=0 blocks, Stripe width=0 blocks
    1966080 inodes, 7864320 blocks
    393216 blocks (5.00%) reserved for the super user
    First data block=0
    Maximum filesystem blocks=4294967296
    240 block groups
    32768 blocks per group, 32768 fragments per group
    8192 inodes per group
    Superblock backups stored on blocks:
    32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208,
    4096000
    
    Allocating group tables: done
    Writing inode tables: done
    Creating journal (32768 blocks): done
    Writing superblocks and filesystem accounting information: done
    
    mke2fs 1.42.5 (29-Jul-2012)
    
    ========================================
    Create Primary Partition #2 (ext4, 30.00 GiB) on /dev/sda  00:00:02    ( SUCCESS )
         	
    create empty partition  00:00:00    ( SUCCESS )
         	
    path: /dev/sda2
    start: 62,916,608
    end: 125,831,167
    size: 62,914,560 (30.00 GiB)
    set partition type on /dev/sda2  00:00:00    ( SUCCESS )
         	
    new partition type: ext4
    create new ext4 file system  00:00:02    ( SUCCESS )
         	
    mkfs.ext4 -j -O extent -L "OS2a" /dev/sda2
         	
    Filesystem label=OS2a
    OS type: Linux
    Block size=4096 (log=2)
    Fragment size=4096 (log=2)
    Stride=0 blocks, Stripe width=0 blocks
    1966080 inodes, 7864320 blocks
    393216 blocks (5.00%) reserved for the super user
    First data block=0
    Maximum filesystem blocks=4294967296
    240 block groups
    32768 blocks per group, 32768 fragments per group
    8192 inodes per group
    Superblock backups stored on blocks:
    32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208,
    4096000
    
    Allocating group tables: done
    Writing inode tables: done
    Creating journal (32768 blocks): done
    Writing superblocks and filesystem accounting information: done
    
    mke2fs 1.42.5 (29-Jul-2012)
    
    ========================================
    Create Primary Partition #3 (ext4, 536.17 GiB) on /dev/sda  00:00:05    ( SUCCESS )
         	
    create empty partition  00:00:00    ( SUCCESS )
         	
    path: /dev/sda3
    start: 125,831,168
    end: 1,250,263,039
    size: 1,124,431,872 (536.17 GiB)
    set partition type on /dev/sda3  00:00:01    ( SUCCESS )
         	
    new partition type: ext4
    create new ext4 file system  00:00:04    ( SUCCESS )
         	
    mkfs.ext4 -j -O extent -L "HomeA" /dev/sda3
         	
    Filesystem label=HomeA
    OS type: Linux
    Block size=4096 (log=2)
    Fragment size=4096 (log=2)
    Stride=0 blocks, Stripe width=0 blocks
    35143680 inodes, 140553984 blocks
    7027699 blocks (5.00%) reserved for the super user
    First data block=0
    Maximum filesystem blocks=4294967296
    4290 block groups
    32768 blocks per group, 32768 fragments per group
    8192 inodes per group
    Superblock backups stored on blocks:
    32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208,
    4096000, 7962624, 11239424, 20480000, 23887872, 71663616, 78675968,
    102400000
    
    Allocating group tables: done
    Writing inode tables: done
    Creating journal (32768 blocks): done
    Writing superblocks and filesystem accounting information: done
    
    mke2fs 1.42.5 (29-Jul-2012)
    
    ========================================
    Create Primary Partition #4 (ext4, 30.00 GiB) on /dev/sdb  00:00:02    ( ERROR )
         	
    create empty partition  00:00:01    ( SUCCESS )
         	
    path: /dev/sdb1
    start: 2,048
    end: 62,916,607
    size: 62,914,560 (30.00 GiB)
    set partition type on /dev/sdb1  00:00:01    ( SUCCESS )
         	
    new partition type: ext4
    create new ext4 file system  00:00:00    ( ERROR )
         	
    mkfs.ext4 -j -O extent -L "OS1b" /dev/sdb1
         	
    mke2fs 1.42.5 (29-Jul-2012)
    /dev/sdb1 is apparently in use by the system; will not make a filesystem here!
    
    ========================================
    Create Primary Partition #5 (ext4, 30.00 GiB) on /dev/sdb
    
    ========================================
    Create Primary Partition #6 (ext4, 536.17 GiB) on /dev/sdb
    
    ========================================
    Create Primary Partition #7 (linux-swap, 16.00 GiB) on /dev/sdb
    
    ========================================
    As you can see, my /dev/sdb is a bit larger than my /dev/sda. The drives used to be identical, but one of my 640 GB drives was returned (under warranty). Western Digital sent me a 750 GB drive. Apparently they're out of the 640's.

    My plan is to have three RAID1 partitions -- one for Ubuntu 13.04 root, one for a future Ubuntu release, and one for /home. Swap goes in the extra space on /dev/sdb, and is not part of the RAID.


    EDIT: follow-up: The pull-down menu in GParted now shows that I have a /dev/md127, 8.00 GiB in size, in addition to the /dev/sda and /dev/sdb that I expect. It also appears in /proc/mdstat:

    Code:
    ubuntu@ubuntu:~$ cat /proc/mdstat
    
    Personalities : [raid1] 
    md127 : active raid1 sdb1[1]
          8384448 blocks super 1.2 [2/1] [_U]
          
    unused devices: <none>

    HOW did this /dev/md127 get created, and why is it being given RAID status when I haven't even started with the RAID part of my partitioning? Why is it 8.00 GiB? This matches the size of my old swap partition (which was on the RAID), but it does not match the size of any of the new partitions I am trying to create.
    Last edited by ladasky; June 12th, 2013 at 08:54 PM.

  6. #6
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    Re: RAID woes, can't repartition my hard drives

    Did you try writing a new partition table on both? Try from the terminal, not with Gparted (shouldn't make a difference, but give it a shot):
    Code:
    sudo parted /dev/sda
    mklabel msdos (or gpt if you prefer gpt table)
    select /dev/sdb
    mklabel msdos
    quit
    After that reboot and try again creating partitions with Gparted.

    Note that if you use gpt table you have to make a small 1MiB partition with NO filesystem and with the bios_grub flag set on it. This is needed for grub2 to install correctly on gpt disks.

    Also, did you check if you have some fakeraid meta data on the disks? Just in case, try:
    Code:
    sudo dmraid -Er /dev/sda
    sudo dmraid -Er /dev/sdb
    Remove any meta data found.
    Darko.
    -----------------------------------------------------------------------
    Ubuntu 12.04 LTS 64bit & Windows 7 Ultimate 64bit

  7. #7
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    Re: RAID woes, can't repartition my hard drives

    Quote Originally Posted by darkod View Post
    Did you check if you have some fakeraid meta data on the disks? Just in case, try:
    Code:
    sudo dmraid -Er /dev/sda
    sudo dmraid -Er /dev/sdb
    Remove any meta data found.
    When I first started using RAID about three years ago, I read about dmraid/fakeraid and chose not to use it. Still, I checked, and the system was clear of any fakeraid data.

    Code:
    ubuntu@ubuntu:~$ sudo dmraid -Er /dev/sda
    no raid disks and with names: "/dev/sda"
    ubuntu@ubuntu:~$ sudo dmraid -Er /dev/sdb
    no raid disks and with names: "/dev/sdb"
    ubuntu@ubuntu:~$ sudo parted /dev/sda
    Quote Originally Posted by darkod View Post
    Did you try writing a new partition table on both? Try from the terminal, not with Gparted (shouldn't make a difference, but give it a shot):
    Code:
    sudo parted /dev/sda
    mklabel msdos (or gpt if you prefer gpt table)
    select /dev/sdb
    mklabel msdos
    quit
    After that reboot and try again creating partitions with Gparted.

    Note that if you use gpt table you have to make a small 1MiB partition with NO filesystem and with the bios_grub flag set on it. This is needed for grub2 to install correctly on gpt disks.
    OK, so after I stopped and zeroed the mysterious /dev/md127 once again, I was able to execute the parted commands that you recommended. Also, THANK YOU for the hint that gpt needs an unformatted partition for Grub2, I included one on each drive. (I needed more than four partitions after all!) For some reason, I was unable to set the bios-grub flags in my newly-created partitions until after a reboot, but that was OK.

    On reboot, I have the following:

    Code:
    ubuntu@ubuntu:~$ sudo parted -l
    
    Model: ATA WDC WD6401AALS-0 (scsi)
    Disk /dev/sda: 640GB
    Sector size (logical/physical): 512B/512B
    Partition Table: gpt
    
    Number  Start   End     Size    File system  Name  Flags
     1      1049kB  2097kB  1049kB                     bios_grub
     2      2097kB  32.2GB  32.2GB  ext4
     3      32.2GB  64.4GB  32.2GB  ext4
     4      64.4GB  640GB   576GB   ext4
    
    
    Model: ATA WDC WD7501AALS-0 (scsi)
    Disk /dev/sdb: 750GB
    Sector size (logical/physical): 512B/512B
    Partition Table: gpt
    
    Number  Start   End     Size    File system     Name  Flags
     1      1049kB  2097kB  1049kB                        bios_grub
     2      2097kB  32.2GB  32.2GB  ext4
     3      32.2GB  64.4GB  32.2GB  ext4
     4      64.4GB  640GB   576GB   ext4
     5      640GB   657GB   17.2GB  linux-swap(v1)
    
    
    Warning: Unable to open /dev/sr0 read-write (Read-only file system).  /dev/sr0
    has been opened read-only.
    Error: Can't have a partition outside the disk!
    I think that I'm finally ready for mdadm. When I accomplish that, I will mark this task as Solved.

  8. #8
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    Re: RAID woes, can't repartition my hard drives

    My efforts with mdadm succeeded, and I am ready to mark this thread as Solved. (Hey, where exactly did the "mark as solved" button go?) Thanks as always, darkod.

    Unfortunately: the whole reason that I was going through this exercise was to try to install 13.04 on a RAID1, and it STILL DOES NOT WORK. Just as before, I am getting a "fatal error" at the grub-install stage. I've just spent six weeks going in a giant circle. Actually, I've taken a step backwards -- now that I've killed my original array, and no longer have a working 12.04 system on my hard drive!

    Darkod, you were also the person who helped me the most in that previous thread. I'm going to try one more idea... and then revive the thread if I have more questions. See you there?
    Last edited by ladasky; June 13th, 2013 at 12:36 AM. Reason: mark as solved?

  9. #9
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    Re: RAID woes, can't repartition my hard drives

    I marked it [SOLVED] for you. Hopefully, one of these will be helpful:
    http://ubuntuforums.org/showthread.php?t=2151638
    http://ubuntuforums.org/showthread.php?t=2121377
    Linux User #415691 Ubuntu User #8629
    Iowa Team (LoCo): [Wiki] [Launchpad]
    IRC channel: #ubuntu-us-ia on irc.freenode.net

  10. #10
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    Re: RAID woes, can't repartition my hard drives

    Thanks, Iowan. I'll subscribe to those threads and, hopefully, I'll remember to look through my subscribed threads the next time I have one to mark.

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