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This system has a boot partition on a dm-raid device.

I updated the system by standard methods from an older Ubuntu to the latest LTS. Now, if the kernel is updated by "apt-get upgrade", the new kernel will not load. Nor are the entries listed in the GRUB boot screen.

I have determined that update-grub works as I would expect, updating the partition mounted at /boot. However, when I boot it, GRUB reads the root drive /boot folder. It does not mount the raid isw_dbbbejgeca_Volume0p1 to /boot before starting up.

If I copy the contents of the mounted /boot drive to a folder, then unmount it and copy all the contents to the root drive /boot folder, the system will then boot the new kernels and show all the updates in the GRUB menu.

I need help to make sure GRUB will mount the raid based boot partition.

Next are some output from boot-repair tool.

 Boot Info Script e7fc706 + Boot-Repair extra info      [Boot-Info 23Nov2014]

============================= Boot Info Summary: ===============================

 => No boot loader is installed in the MBR of /dev/sdc.

    Operating System:  Ubuntu 14.04.1 LTS 
    Boot files:        /etc/fstab

============================ Drive/Partition Info: =============================

"blkid" output: ________________________________________________________________

Device           UUID                                   TYPE       LABEL

/dev/mapper/isw_dbbbejgeca_Volume0p1 840df97f-7154-49a3-aa9c-02bd092d416c   ext2       
/dev/mapper/isw_dbbbejgeca_Volume0p5 M9ln25-ua43-3S0c-xWeT-8Ejd-tk2U-kp5nNG LVM2_member 
/dev/mapper/server01-root c16300cf-e8da-4e2b-b34a-45d8fc12fb44   ext4       
/dev/mapper/server01-swap_1 b67b89f9-a131-46f8-b29b-0eb450e18a6a   swap       
/dev/sda                                                isw_raid_member 
/dev/sdb                                                isw_raid_member 
/dev/sdc1        08652f68-2f8e-4044-8c0b-9b33cb623bba   ext4       

========================= "ls -l /dev/disk/by-id" output: ======================

total 0
lrwxrwxrwx 1 root root  9 Jan 19 23:21 ata-OCZ-VERTEX_30565XA328O39Y3Y2A6G -> ../../sda
lrwxrwxrwx 1 root root  9 Jan 19 23:21 ata-OCZ-VERTEX_OH43J28TQB2Q7T570144 -> ../../sdb
lrwxrwxrwx 1 root root  9 Jan 19 23:21 ata-WDC_WD20EARS-00MVWB0_WD-WCAZA1927955 -> ../../sdc
lrwxrwxrwx 1 root root 10 Jan 19 23:11 ata-WDC_WD20EARS-00MVWB0_WD-WCAZA1927955-part1 -> ../../sdc1
lrwxrwxrwx 1 root root 10 Jan 19 23:11 dm-name-isw_dbbbejgeca_Volume0 -> ../../dm-0
lrwxrwxrwx 1 root root 10 Jan 19 23:21 dm-name-isw_dbbbejgeca_Volume0p1 -> ../../dm-1
lrwxrwxrwx 1 root root 10 Jan 19 23:21 dm-name-isw_dbbbejgeca_Volume0p2 -> ../../dm-2
lrwxrwxrwx 1 root root 10 Jan 19 23:11 dm-name-isw_dbbbejgeca_Volume0p5 -> ../../dm-3
lrwxrwxrwx 1 root root 10 Jan 19 23:21 dm-name-server01-root -> ../../dm-4
lrwxrwxrwx 1 root root 10 Jan 19 23:21 dm-name-server01-swap_1 -> ../../dm-5
lrwxrwxrwx 1 root root 10 Jan 19 23:11 dm-uuid-DMRAID-isw_dbbbejgeca_Volume0 -> ../../dm-0
lrwxrwxrwx 1 root root 10 Jan 19 23:21 dm-uuid-LVM-P3d2Ucn1G9Wx7NUE0e5vNgabXjXrfHIe555TD7gDdpyqH82c1sP9ofmm1Ook2SIS -> ../../dm-4
lrwxrwxrwx 1 root root 10 Jan 19 23:21 dm-uuid-LVM-P3d2Ucn1G9Wx7NUE0e5vNgabXjXrfHIeA3DF0518wh8WsbW9i1cbOrcywyAwRUAg -> ../../dm-5
lrwxrwxrwx 1 root root 10 Jan 19 23:21 dm-uuid-part1-DMRAID-isw_dbbbejgeca_Volume0 -> ../../dm-1
lrwxrwxrwx 1 root root 10 Jan 19 23:21 dm-uuid-part2-DMRAID-isw_dbbbejgeca_Volume0 -> ../../dm-2
lrwxrwxrwx 1 root root 10 Jan 19 23:11 dm-uuid-part5-DMRAID-isw_dbbbejgeca_Volume0 -> ../../dm-3
lrwxrwxrwx 1 root root 10 Jan 19 23:21 raid-isw_dbbbejgeca_Volume0-part1 -> ../../dm-1
lrwxrwxrwx 1 root root 10 Jan 19 23:21 raid-isw_dbbbejgeca_Volume0-part2 -> ../../dm-2
lrwxrwxrwx 1 root root 10 Jan 19 23:11 raid-isw_dbbbejgeca_Volume0-part5 -> ../../dm-3
lrwxrwxrwx 1 root root  9 Jan 19 23:21 wwn-0x50014ee2052521f1 -> ../../sdc
lrwxrwxrwx 1 root root 10 Jan 19 23:11 wwn-0x50014ee2052521f1-part1 -> ../../sdc1

========================= "ls -R /dev/mapper/" output: =========================

/dev/mapper:
control
isw_dbbbejgeca_Volume0
isw_dbbbejgeca_Volume0p1
isw_dbbbejgeca_Volume0p2
isw_dbbbejgeca_Volume0p5
server01-root
server01-swap_1

================================ Mount points: =================================

Device           Mount_Point              Type       Options

/dev/mapper/isw_dbbbejgeca_Volume0p1 /boot                    ext2       (rw)
/dev/mapper/server01-root /                        ext4       (rw,errors=remount-ro)
/dev/sdc1        /home/backup/repos       ext4       (rw)


=========================== server01-root/etc/fstab: ============================

--------------------------------------------------------------------------------
# /etc/fstab: static file system information.
#
# Use 'blkid -o value -s UUID' to print the universally unique identifier
# for a device; this may be used with UUID= as a more robust way to name
# devices that works even if disks are added and removed. See fstab(5).
#
#                
proc            /proc           proc    nodev,noexec,nosuid 0       0
/dev/mapper/server01-root /               ext4    errors=remount-ro 0       1
/dev/mapper/isw_dbbbejgeca_Volume0p1 /boot           ext2    defaults        0       2
/dev/mapper/server01-swap_1 none            swap    sw              0       0
/dev/scd0       /media/floppy0  auto    rw,user,noauto,exec,utf8 0       0
UUID=08652f68-2f8e-4044-8c0b-9b33cb623bba   /home/backup    ext4    defaults    0   2   

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

========= Devices which don't seem to have a corresponding hard drive: =========

{All_DMRaid} 

=================== os-prober:
/dev/mapper/server01-root:The OS now in use - Ubuntu 14.04.1 LTS CurrentSession:linux

=================== blkid:
/dev/sda: TYPE="isw_raid_member"
/dev/sdb: TYPE="isw_raid_member"
/dev/mapper/isw_dbbbejgeca_Volume0p1: UUID="840df97f-7154-49a3-aa9c-02bd092d416c" TYPE="ext2"
/dev/mapper/isw_dbbbejgeca_Volume0p5: UUID="M9ln25-ua43-3S0c-xWeT-8Ejd-tk2U-kp5nNG" TYPE="LVM2_member"
/dev/mapper/server01-root: UUID="c16300cf-e8da-4e2b-b34a-45d8fc12fb44" TYPE="ext4"
/dev/mapper/server01-swap_1: UUID="b67b89f9-a131-46f8-b29b-0eb450e18a6a" TYPE="swap"

[dmraid -sa -c] isw_dbbbejgeca_Volume0
Set sda as corresponding disk of mapper/server01-root

1 disks with OS, 1 OS : 1 Linux, 0 MacOS, 0 Windows, 0 unknown type OS.

Warning: extended partition does not start at a cylinder boundary.
DOS and Linux will interpret the contents differently.

sfdisk: ERROR: sector 500734 does not have an msdos signature
Warning: extended partition does not start at a cylinder boundary.
DOS and Linux will interpret the contents differently.
Warning: invalid flag 0x616f of partition table 5 will be corrected by w(rite)
Warning: invalid flag 0x616f of partition table 5 will be corrected by w(rite)

=================== /etc/grub.d/ :
drwxr-xr-x  2 root    root        4096 Oct 21 10:25 grub.d
total 76
-rwxr-xr-x 1 root root  9761 Oct 28 09:08 00_header
-rwxr-xr-x 1 root root  6058 May  8  2014 05_debian_theme
-rwxr-xr-x 1 root root 11608 Nov  3 18:39 10_linux
-rwxr-xr-x 1 root root 10412 May 15  2014 20_linux_xen
-rwxr-xr-x 1 root root  1992 Mar 12  2014 20_memtest86+
-rwxr-xr-x 1 root root 11692 May 15  2014 30_os-prober
-rwxr-xr-x 1 root root  1416 May 15  2014 30_uefi-firmware
-rwxr-xr-x 1 root root   214 Oct  6  2010 40_custom
-rwxr-xr-x 1 root root   216 May 15  2014 41_custom
-rw-r--r-- 1 root root   483 Oct  6  2010 README

=================== /etc/default/grub :

# If you change this file, run 'update-grub' afterwards to update
# /boot/grub/grub.cfg.
# For full documentation of the options in this file, see:
#   info -f grub -n 'Simple configuration'

GRUB_DEFAULT=0
#GRUB_HIDDEN_TIMEOUT=0
GRUB_HIDDEN_TIMEOUT_QUIET=true
GRUB_TIMEOUT=2
GRUB_DISTRIBUTOR=`lsb_release -i -s 2> /dev/null || echo Debian`
GRUB_CMDLINE_LINUX_DEFAULT="ipv6.disable=1 quiet"
GRUB_CMDLINE_LINUX=""

# Uncomment to enable BadRAM filtering, modify to suit your needs
# This works with Linux (no patch required) and with any kernel that obtains
# the memory map information from GRUB (GNU Mach, kernel of FreeBSD ...)
#GRUB_BADRAM="0x01234567,0xfefefefe,0x89abcdef,0xefefefef"

# Uncomment to disable graphical terminal (grub-pc only)
#GRUB_TERMINAL=console

# The resolution used on graphical terminal
# note that you can use only modes which your graphic card supports via VBE
# you can see them in real GRUB with the command `vbeinfo'
#GRUB_GFXMODE=640x480

# Uncomment if you don't want GRUB to pass "root=UUID=xxx" parameter to Linux
#GRUB_DISABLE_LINUX_UUID=true

# Uncomment to disable generation of recovery mode menu entries
#GRUB_DISABLE_RECOVERY="true"

# Uncomment to get a beep at grub start
#GRUB_INIT_TUNE="480 440 1"

/boot detected in the fstab of mapper/server01-root: /dev/mapper/isw_dbbbejgeca_Volume0p1  (mapper/isw_dbbbejgeca_Volume0p1)

=================== mapper/server01-root/etc/mdadm/mdadm.conf :
# 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

# 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 

# instruct the monitoring daemon where to send mail alerts
MAILADDR root

# definitions of existing MD arrays
ARRAY metadata=imsm UUID=a624f30e:6036d720:067d7817:ea238d58
ARRAY /dev/md/Volume0 container=a624f30e:6036d720:067d7817:ea238d58 member=0 UUID=03fe4a37:77503687:17ce6055:d75a6ac2

=================== PARTITIONS & DISKS:
mapper/server01-root    : sdb,  .
mapper/isw_dbbbejgeca_Volume0p1 : mapper/isw_dbbbejgeca_Volume0,    /boot.
sdb : not-GPT,  BIOSboot-not-needed,    has-no-EFIpart,     not-usb,    has-os, 2048 sectors * 512 bytes
sda : not-GPT,  BIOSboot-not-needed,    has-no-EFIpart,     not-usb,    no-os,  2048 sectors * 512 bytes
mapper/isw_dbbbejgeca_Volume0   : not-GPT,  BIOSboot-not-needed,    has-no-EFIpart,     not-usb,    no-os,  2048 sectors * 512 bytes

=================== mount:
/dev/mapper/server01-root on / type ext4 (rw,errors=remount-ro)
/dev/mapper/isw_dbbbejgeca_Volume0p1 on /boot type ext2 (rw)

=================== ls:
Disk /dev/mapper/isw_dbbbejgeca_Volume0p1 doesn't contain a valid partition table
fdisk: unable to read /dev/mapper/isw_dbbbejgeca_Volume0p2: Inappropriate ioctl for device

=================== df -Th:
Filesystem                           Type      Size  Used Avail Use% Mounted on
/dev/mapper/server01-root             ext4      225G  209G  4.7G  98% /
/dev/mapper/isw_dbbbejgeca_Volume0p1 ext2      229M  123M   94M  57% /boot
/dev/sdc1                            ext4      1.8T  573G  1.2T  33% /home/backup

=================== fdisk -l:

Disk /dev/sda: 128.0 GB, 128035676160 bytes
255 heads, 63 sectors/track, 15566 cylinders, total 250069680 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x00087dad

Device Boot      Start         End      Blocks   Id  System
/dev/sda1             512      500223      249856   83  Linux
/dev/sda2          500734   500130303   249814785    5  Extended
/dev/sda5   ?   809621278  1718751574   454565148+  32  Unknown

Disk /dev/sdb: 128.0 GB, 128035676160 bytes
255 heads, 63 sectors/track, 15566 cylinders, total 250069680 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x99e561ed

Device Boot      Start         End      Blocks   Id  System

Disk /dev/mapper/isw_dbbbejgeca_Volume0: 256.1 GB, 256066715648 bytes
255 heads, 63 sectors/track, 31131 cylinders, total 500130304 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 131072 bytes / 262144 bytes
Disk identifier: 0x00087dad

Device Boot      Start         End      Blocks   Id  System
/dev/mapper/isw_dbbbejgeca_Volume0p1             512      500223      249856   83  Linux
/dev/mapper/isw_dbbbejgeca_Volume0p2          500734   500130303   249814785    5  Extended
Partition 2 does not start on physical sector boundary.
/dev/mapper/isw_dbbbejgeca_Volume0p5          500736   500130303   249814784   8e  Linux LVM

Disk /dev/mapper/isw_dbbbejgeca_Volume0p1: 255 MB, 255852544 bytes
255 heads, 63 sectors/track, 31 cylinders, total 499712 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 131072 bytes / 262144 bytes
Disk identifier: 0x00000000


Partition outside the disk detected.


=================== Suggested repair
The default repair of the Boot-Repair utility would purge 
(in order to enable-raid enable-lvm) and reinstall the 
grub2 of mapper/server01-root into the MBR of sdb, using 
the following options:
        mapper/isw_dbbbejgeca_Volume0p1/boot,
The boot flag would be placed on sdc1.
Additional repair would be performed:
        unhide-bootmenu-10s


=================== Advice in case of suggested repair
Warning: continuing without internet would leave your system 
unbootable. Please connect internet.
Do you want to continue?


=================== Final advice in case of suggested repair
Please do not forget to make your BIOS boot on sdb (128GB) disk!


=================== User settings
The settings chosen by the user will not act on the boot.

I am not sure of the suggestions.

The boot flag would be placed on sdc1.

sdc1 is a backup disk, it will not be there always. I don't need a boot setup on that disk I think.

I am worried it may become unbootable. This boot-repair requires internet, but that server will not be accessing the internet.

So, I ask you to share some grub commands to do the other steps:

 purge and reinstall the grub2 of mapper/server01-root into the MBR of sdb, using the following options:
    mapper/isw_dbbbejgeca_Volume0p1/boot,
 Additional repair would be performed:
    unhide-bootmenu-10s
1

This is described on the Ubuntu wiki. Maybe should have asked over there in first place. Sorry. But in case for future visitors. Here is the link. However, the raid configuration did not allow installation on a /dev/sdb as indicated by boot-repair. The install must go to the main raid volume. Here is another link about that.

And here the short version:

sudo apt-get update
sudo apt-get purge grub-common
sudo apt-get install grub-pc  #Choose /dev/mapper/isw_dbbbejgeca_Volume0
sudo update-grub
sudo grub-install /dev/mapper/isw_dbbbejgeca_Volume0
sudo grub-install --recheck /dev/mapper/isw_dbbbejgeca_Volume0

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