Ubuntu – Full install of Ubuntu 12.04 on USB pendrive halts at GRUB prompt

I never got in trouble by using these instructions:
https://wiki.ubuntu.com/Grub2#Recover

First of all, you must start your system from a live cd. Then

"METHOD 3 - CHROOT

This method of installation uses the chroot command to gain access to the broken system's files. Once the chroot command is issued, the LiveCD treats the broken system's / as its own. Commands run in a chroot environment will affect the broken systems filesystems and not those of the LiveCD.

1) Boot to the LiveCD Desktop (Ubuntu 9.10 or later). Please note that the Live CD must be the same as the system you are fixing - either 32-bit or 64-bit (if not then the chroot will fail).

2) Open a terminal (Applications > Accessories > Terminal).

3) Determine your normal system partition - (the switch is a lowercase "L")

sudo fdisk -l

If you aren't sure, run

df -Th  

Look for the correct disk size and ext3 or ext4 format.

4) Mount your normal system partition:

Substitute the correct partition: sda1, sdb5, etc.

sudo mount /dev/sdXX /mnt  

Example: sudo mount /dev/sda1 /mnt

5) Only if you have a separate boot partition: sdYY is the /boot partition designation (for example sdb3)

sudo mount /dev/sdYY /mnt/boot 

6) Mount the critical virtual filesystems:

sudo mount --bind /dev  /mnt/dev
sudo mount --bind /dev/pts  /mnt/dev/pts
sudo mount --bind /proc /mnt/proc
sudo mount --bind /sys  /mnt/sys 

7) Chroot into your normal system device:

sudo chroot /mnt 

8) If there is no /boot/grub/grub.cfg or it's not correct, create one using

update-grub 

9) Reinstall GRUB 2:

Substitute the correct device - sda, sdb, etc. Do not specify a partition number.

grub-install /dev/sdX 

10) Verify the install (use the correct device, for example sda. Do not specify a partition):

sudo grub-install --recheck /dev/sdX 

11) Exit chroot: CTRL-D on keyboard

12) Unmount virtual filesystems:

sudo umount /mnt/dev/pts
sudo umount /mnt/dev
sudo umount /mnt/proc
sudo umount /mnt/sys 

13) If you mounted a separate /boot partition:

sudo umount /mnt/boot 

14) Unmount the LiveCD's /usr directory:

sudo umount /mnt/usr 

15) Unmount last device:

sudo umount /mnt 

16) Reboot.

sudo reboot 

The symptom of being able to see some files but not all on a filesystem with grub usually means that your BIOS is buggy and can't properly handle large drives ( http://tldp.org/HOWTO/Large-Disk-HOWTO-4.html ). What happens is that the BIOS can't read blocks past a certain point in the drive, and so if your root filesystem starts before that limit, but ends after that limit, then some files will be accessible at boot through the BIOS and others won't. The standard way to work around this problem is to create a small /boot/ partition near the beginning of the drive, to ensure that everything that needs to be read through the BIOS, can be.

I would normally expect "out of disk" errors from grub were this the case, and I don't know why we're not seeing those. One way to confirm that the problem is a BIOS limit is to go into your BIOS menus and see what size it lists the drive as being, if it lists it as being less that the actual size, you know your BIOS is buggy. Another way, if your BIOS doesn't list sizes anywhere in its menus, is to run "ls -l" from grub and look at the size listed there. Unfortunately, you can't run "ls -l" from the rescue shell, so you'd need to boot from a grub CD, or have already fixed the problem with a small /boot/ partition, before you could do the check from within grub.