Ubuntu – Unable to boot 12.04 after install on 3TB drive

It's extremely useful to have an "on-the-go" Ubuntu running on USB with full disk encryption. Imagine you can boot up on almost every computer with your USB, and work in your own personalized environment anywhere, without carrying a notebook. I managed to install Ubuntu 16.04 in a USB HDD this way:

1. Download the latest Ubuntu installer.

2. Make a bootable pendrive. I use LiLi on Windows and dd command on Linux. You can google it.

3. Boot up from Ubuntu pendrive. The Ubuntu installer detects the internal HDD and offers to install Ubuntu and keep the other OS, or make a clean install, optionally with encryption. However, this window only shows the internal HDD. If you want to install to USB, you have to select the "Other" option. But it is really hard to setup an encrypted install manually.

4. I did the following: take out my internal HDD from my notebook, and boot up Ubuntu installer again. If the USB drive is connected, but the internal HDD is taken out, the installer will display the USB drive as primary drive and offers to make a clear install with encryption. You can also choose to overwrite your disk before install if you want.

5. Start the installation with your preferred options. Same as usual from now on.

I tested my USB Ubuntu on 5 different computer from old to "new" and it works like a charm. No problem with drivers, not a single error or question window when I boot up on a different PC.

The problem is this, from your post:

sd 6:0:0:0: [sdc] 732566646 4096-byte logical blocks: (3.00 TB/2.72 TiB)

When connecting your disk via USB, the enclosure is translating its 512-byte logical blocks into 4096-byte logical blocks. This completely messes up the partition table created when you used the disk internally (or via the eSATA port). Translations like this make the disk usable with the older MBR partitioning system, and so are fairly common on external disks. In this case, though, it's effectively a bug. IMHO, any translation applied by the enclosure to a USB interface but not to an eSATA interface is a bug, since it locks the disk into use by the interface that was used to partition the disk. (Note that switching from GPT to MBR won't help, since both partition table types define partitions by sector values, which are inconstant between the interface types.) Note that this is a problem with the enclosure's firmware, not in Linux.

You might want to check the documentation (including anything you can find from the enclosure's manufacturer online) for information on disabling this feature. If you're lucky, there'll be a DIP switch or some way to reprogram the USB interface from your computer to disable this translation.

If that fails, your best option, given your needs, is to exchange the enclosure for one that doesn't do this translation, or that applies it to all interfaces. (I'm not sure if it's technically possible to apply such a translation to an eSATA port, though.) You could do this by returning the enclosure to the store or possibly by swapping the disk with another enclosure. If you're lucky, the enclosure will only apply this rule to disks that are over 2TiB in size, so swapping disks with a smaller external disk might fix the problem. Beware, though: Some USB enclosures can't handle over-2TiB disks at all, so you could just make matters worse.

If you can't replace the enclosure, then you'll just have to deal with it -- decide whether you want to use USB or eSATA, tape over the one you don't want to use, and live with it. If you use USB, you'll need to wipe the partition table and repartition the disk.