One SSD instead of two: simpler or not?

My Core i7 machine, named Drake, had two 120Gb SSD drives. I purchased the first one with the machine and put Windows 7 and Ubuntu on it. Then I needed more space to get Mac OS X, so I added a second 120Gb SSD. Mac OS X became a pain, almost unusable because everything was too small. When I reached the point I had to lower screen resolution to get Thunderbird running comfortably, I got rid of Mac OS X. Then Windows 7, upgraded to Windows 8, started to eat up more space so I needed to move Ubuntu to the second SSD.

I ended up with a brittle configuration composed of the ESP (EFI system partition) on the second SSD, Windows 8.1 on the first drive and Ubuntu on the second. I was waiting for a special deal on a 240Gb SSD and finally got one on TigerDirect at the beginning of September 2014. However, purchasing the SSD is only the easy part. Migrating data from two SSD drives to a single one, with Windows 8.1, Ubuntu 14.04 and UEFI in the way, is an incredible source of headache. This page shows how I got it done.

The easy way: reinstall everything

That would have worked ten, maybe even five years ago. Yes, just reinstall Windows, a few drivers, a few programs, put back Ubuntu, perform some settings, fine tune a bit, and enjoy the rebirth of the system, coming back to life and full functionality. Things changed with years, not for good. Now that Microsoft and other hardware manufacturers assume people won’t install by themselves and rather purchase hardware with everything preinstalled and preconfigured, things became more and more time consuming to setup. Just installing Windows 8 takes more than 45 minutes, and although I could obtain a DVD with Windows 8.1, my Windows 8 serial number won’t work with it. I would have had to install Windows 8, then upgrade to Windows 8.1 again!

Then come the drivers. Since I purchased my motherboard before Windows 8 was released, all my motherboard CD has to offer is Windows 7 drivers. So I cannot use the easy auto-install tool performing an unattended setup. I rather have to download every driver separately from Asus, run them, wait, reboot, run the next one, etc. Then there is the NVIDIA driver, requiring 100 Mb of download and yet another installation taking more than five minutes, and yet another reboot. Maybe I chose the wrong motherboard. By sacrificing a few USB ports, S/PDIF audio and maybe some PCI Express slots, maybe I could get something simpler not requiring as many drivers, that would be able to make use of what is prepackaged within Windows. That’s still to be investigated.

Then come the programs. Yes, Ninite can install me many programs automatically but not GNU Emacs, GNU GPG, it won’t configure my Dropbox, resync my Firefox bookmarks, reinitialize my Thunderbird email settings. It won’t link back my Documents, Images, Music and Videos default folders to my data hard drive.

And then come the licenses. How Windows 8.1 activation will behave? Will it happen smoothly, or will Windows decide that this change of SSD is too much and require me to call Microsoft to perform activation by phone, forcing me to exchange, by voice, on a poor channel, tens of nonsensical digits? After Windows 8.1 activation, my DAW, Live from Ableton, also requires authorization. I’m not sure it will reauthorize, since I activated it on my main PC as well as my ultrabook. That means additional hassle.

Bottom line, reinstalling is a pain, and that is just the Windows side. Ubuntu installation is usually smooth, but when a single thing goes bad, it requires hours of Google searches.

This is why I wanted a better way. I was so tired of this tedious process I was considering giving up on this machine and use my ultrabook instead, if data transfer failed. But my ultrabook, with its 128Gb SSD, won’t have enough storage for editing music made of samples or recording/editing Minecraft videos.

Preliminary connection of the new SSD

Before installing the new 240Gb SSD into my system permanently, I wanted to be sure I would be able to transfer my two operating systems (Windows 8.1 and Ubuntu 14.04) and make them boot. I thus only plugged the disk rather than attaching it right away into my case. I fortunately had some free SATA power cables as well as an extra SATA cable and port. That allowed me to connect the new drive without disconnecting the others. This way, it would have been easy to roll back in case of difficulties forcing me to reinstall everything, and then think about another strategy or gather my courage and patience for the full reinstall.

I then booted from a USB stick with a Live installation of Ubuntu 14.04. This was necessary to perform the data transfer on a totally offline, clean, file system.

Before transferring anything on the drive, I ran a SMART self test. For this, I installed smartmontools with apt-get and ran sudo smartctl -t long /dev/sdb. At this time, /dev/sdb was the device of the drive. That took almost an hour, but I could leave this running and do something else.

The self-test found no defects. I learned to do this preliminary step the hard way when I assembled a machine for my parents. The hard drive failed short while I was configuring Windows and I had to RMA it. Performing a self-test may have avoided me a waste of time and some frustration.

The drive being clean from any defect, at least from the point of view of the self test, I moved to the next step: data transfer.

GParted is the king!

A long time ago, my only friend for partitioning and drive transfer was Parition Magic, from PowerQuest, now purchased by Symantec. That time is over, thanks to GParted, a free open source tool that comes with Ubuntu. But that time, my job was pushing GParted to the limits. Here are the operations I needed to perform with it:

  1. Create a GUID Partition Table (GPT) on the new SSD. This is because I want a pure UEFI-based system. But this is not strictly necessary since the drive is far from the 2Tb limit!
  2. Copy the first partition of my second SSD at the beginning of the new drive: this is the ESP.
  3. Copy the first partition of the first SSD: this is the 128Mb system reserved partition of Windows. That copy wasn’t possible, because GParted didn’t know the partition type. I thus left a 128Mb hole declared as Unformatted, to figure out a way out later on. I was hoping Windows could recreate the data on this partition.
  4. Copy the second partition of the first SSD: this was the Windows main partition.
  5. Copy the 40-ish Gb partition of my second SSD at the end of the new drive: this was my home drive from Ubuntu.
  6. Copy the 20-ish Gb partition of my second SSD at the bottom of the free space on new drive: this was my main Ubuntu installation.
  7. Create an extra 20 Gb partition on the new drive in case I would like to give a shot to a new Linux distribution.
  8. Create a 16Gb swap space on the new drive for Ubuntu’s use.
  9. Resize my Windows main partition to take the rest of the space.

Phew!This long sequence gathering pieces from different sources reminds me of infusion crafting in the Thaumcraft mod of Minecraft, where essentias and items are combined together on an altar to craft powerful magical objects.

I hoped that sequence would work, but that failed at step 5. For no obvious reason, GParted wasn’t able to copy my Ubuntu home drive at the end of the new SSD! I had to leave an 8Mb gap and then resize the partition to fill it. I then performed, one by one, the other operations. That was a quite tedious job, because the mouse pointer was too small and impossible to enlarge without a system hack (Ubuntu bug since 11.10! They chose to remove the option to resize mouse pointer rather than fixing the issue.) and sometimes clicking was opening the menu and closing it right away rather than leaving it open.

Following image gives the final layout. Isn’t that great? Not sure at all this is simpler with one drive than with two, after all…


After this transfer process, I tried to recreate the entries in my UEFI’s NVRAM, using efibootmgr, for Windows and Ubuntu. I then unplugged the SATA cables of my two 120Gb SSD drives from my motherboard and rebooted the PC. I won’t state the exact commands I used here, because that just failed. System wasn’t booting at all.

Fixing Ubuntu

Back to my Ubuntu live USB, after at least five attempts because my motherboard is apparently defective and misses the F8 key from time to time and the need to jump into Setup and change the boot order from there to boot the UEFI USB stick. Boot time with that Asus board is desperately long. Waiting 15 to 20 seconds from power up to boot loader is a shame when knowing it takes less than 1 second on a 300$ laptop! But the laptop lacks storage expandability I need, so I am always stuck on one end or another.

Then comes the fun part. I am pretty surprised there is no easier ways to restore GRUB than the following. I read about boot-repair, but it is just missing, probably yet another PPA to copy/paste and install. Anyway, I ended up getting it to work.

First I found the partition where Ubuntu was installed, /dev/sda5, and mounted it: sudo mkdir /media/ubuntu && sudo mount -t ext4 /dev/sda5 /media/ubuntu. I did the same with my ESP: sudo mkdir /media/efi && sudo mount -t vfat /dev/sda1 /media/efi.

Second step was to establish bindings:

sudo mount –rbind /dev /media/ubuntu/dev
sudo mount –rbind /proc /media/ubuntu/proc
sudo mount –rbind /sys /media/ubuntu/sys
sudo mount –rbind /media/efi /media/ubuntu/boot/efi

That caused some directories inside my Ubuntu mount to mirror exactly the top level directories.

Then I had to chroot into my Ubuntu, using

sudo chroot /media/ubuntu

After all this, system was behaving a bit the same way as if I started a shell on my Ubuntu setup. From this, I tried

sudo upgrade-grub2

That just updated GRUB’s entries, not the EFI one, so didn’t fix the boot.

Then I tried

sudo grub-install

If I remember well, no arguments were necessary, and that fixed my GRUB EFI and added back the Ubuntu entry to NVRAM. This worked only after /boot/efi was correctly referring to my ESP. Note however that for this to work fully, the USB live Ubuntu had to be booted in UEFI mode, not MBR default mode.

A reboot later, I was starting my Ubuntu setup, fully intact and working! Half of the transfer done! Not quite…

Windows was failing to boot and Ubuntu’s update-grub wasn’t detecting Windows anymore. Quite bad.

Windows: desperately dead

Windows, on the other hand, wasn’t booting at all. It was showing a blue screen suggesting me to use the repair tools from Windows DVD. Last time I did this, the tools ran for at least one minute and bailed out, so I had to do a complete refresh which ended up wiping everything and leaving only applications from the Windows store. If I have to choose between such a messed-up repair and a clean install, I would bet for the second option.

Before entering into this reinstall nightmare once again, I tried to recover the reserved partition. For this, I plugged back my Windows 120Gb SSD and booted from my live USB stick to make sure Windows would not kick in and see two copies of itself (one on the old, one on the new SSD). If Windows sees two copies of itself, it changes the disk ID of one copy. If the new drive is changed, everything is messed up and Windows cannot boot anymore, until a refresh is done (and then everything is messed up again!). Back to my live USB, I used DD to transfer the bytes of the old reserved partition to the new one. I also made sure the new /dev/sda2 reserved partition was marked as such in GParted, by modifying the flags. That changed nothing.

The post How to repair the EFI Bootloader in Windows 8 literally saved me hours of work! This gives a procedure that allows to fix the boot loader. The main idea is to log into console from Windows DVD and run bootrec /fixboot command from directory EFI\Microsoft\Boot\ of the ESP, followed by bcdboot  with a couple of arguments, again from the ESP. Luckily, I had my ultrabook, which was quite handy to check the page while I was running the commands on my primary PC.

That solved the issue and allowed me to boot into Windows 8.1! PHEW! Quite a nice step forward.

GRUB not detecting Windows

Now that my machine was able to boot into both Windows and Linux, one could wonder what was missing. Well, I had no easy way to choose which operating system to boot at startup. Originally, GRUB was offering me an option to boot into Windows or Ubuntu. After the transfer, it was only seeing Ubuntu.

I found procedures to manually add an entry for Windows but that involved finding and copy/pasting drive UUID and probably redoing the change on each kernel update. I didn’t want that. Another possibility was to install an alternative EFI boot loader like rEFInd, but these have tendency to display many unwanted icons doing nothing. I got enough trouble with this while fiddling with triple boot (Windows, Linux, Mac OS X).

There was absolutely no way out. People were doing the manual addition of Windows or that was working out of the box. I had to spend more than 45 minutes inspecting the os-prober script and walking through it! By looking at the script and its logs in /var/log/syslog, I manage to find out it was skipping my ESP because the partition was not flagged as Boot! I fixed that from GParted, reran sudo update-grub and tada! GRUB was seeing Windows!

This is NOT the end!

Then I had to proceed with the hardware installation of the new drive. Since I was too impatient to get a SSD, I ended up with an ill-designed system. If I had waited another year before purchasing my Core i7 PC, I would have got a superb case with support for SSD drives. Now I have a CoolerMaster kind of case with only standard 3.5″ drive bays and need to fiddle with SSD brackets. Screwing the SSD drive in this is a painful process of trial and error. Then the assembly doesn’t fit well with the screwless mechanism of the case. This somewhat holds in place, but that’s not smooth installation like a regular 3.5″ drive.

Some more fiddling later, my new SSD was plugged back into my PSU and motherboard, and I got rid of the extra two SATA cables. I stored them away; they will be useful sooner than later, because my two 120Gb SSD won’t remain unused.

I plan to put one of them into my HTPC, which will be another adventure of its own. My HTPC has only four SATA ports, all used up, so I will have to get rid of one hard drive.