Moving a Linux installation to a new drive and encrypting it

I needed to change out the drive in my light laptop for a bigger one. Of course I didn’t want the hassle of OS reinstallation [1], so I decided to move my Manjaro installation from the drive to the other. My install was, regrettably, unencrypted [2] - I wanted to fix that during the move.

I’ve succeeded in both tasks (moving and encryption) after a fair bit of struggle and research. Below you’ll find my process. Even though I’m working with Manjaro here, the process should require little adjustment for other Linux distributions.

Oh, and I’m assuming the setup with UEFI and a GPT partition table on the drive, instead of the old BIOS and MBR.

Copying the old partitions

The laptop I was upgrading holds just one M2 SSD drive. The old drive is a SATA M2, the new one is NVME [3]. In this case I could put the empty/new drive in, and attach the old one over USB3 with an adapter [4], and copy the partitions directly.

Instead, I left the old drive in and attached an external HDD over USB3, in order to pull images from the former drive onto the latter.

I’ve booted the laptop from a live USB, so that the system I wanted to copy wasn’t running.

My system had three partitions:

  • /dev/sda1 - the EFI partition

  • /dev/sda2 - the /boot partition, holding the GRUB config and Linux kernels [5]

  • /dev/sda3 - the root partition, holding the Manjaro installation and my data

You can check out yours with lsblk.

Create images of your partitions with the dd command, like so [6]:

sudo dd if=/dev/sda1 of=/run/media/manjaro/the_external_drive/efi_partition.bin bs=4M status=progress
sudo dd if=/dev/sda2 of=/run/media/manjaro/the_external_drive/boot_partition.bin bs=4M status=progress
sudo dd if=/dev/sda3 of=/run/media/manjaro/the_external_drive/root_partition.bin bs=4M status=progress

If you don’t have a dedicated partition for /boot and it’s just part of your main partition, just copy the files from your /boot (skipping /boot/efi) to the external drive.

Preparing the new drive

With the old partition images on the external drive, you can swap out the old internal drive for the new one.

Next, you should partition it (I used GParted) with the same or bigger partition sizes than you had before. The types/filesystems of the partitions you create don’t matter, because they’ll be overwritten when copying from the images.

If you didn’t start going through this tutorial with a partition for /boot, please create a 512 megabyte ext4 partition for it. You’ll be able to copy your old files to it when we mount it later on.

You should probably set the flags boot and esp flags on your EFI partition. Flags are kept in the partition table, not in the partitions themselves. I don’t know if these flags are strictly necessary, though [7].

After the partitioning, I ended up with this layout (from lsblk):

# ...omitted lines...
# manjaro live USB
sda           8:0    1  28.7G  0 disk /run/miso/bootmnt
├─sda1        8:1    1   2.4G  0 part
└─sda2        8:2    1     4M  0 part
# the external drive holding the partition images
sdb           8:16   0   1.8T  0 disk
└─sdb1        8:17   0   1.8T  0 part /run/media/manjaro/Seagate Backup Plus Drive
# the new drive
nvme0n1     259:0    0 953.9G  0 disk
├─nvme0n1p1 259:4    0   200M  0 part  # will be /boot/efi
├─nvme0n1p2 259:5    0   512M  0 part  # will be /boot
└─nvme0n1p3 259:6    0 953.2G  0 part  # will hold the encrypted root partition

Preparing LVM in LUKS

Note that all (or most) the code is also available as scripts on my repo - moving partitions to the new layout, mounting for chroot, adjusting configs and building GRUB.

First, set up some variables you’ll be using throughout the process. You’ll need change these so they match your system and personal preferences, of course.

export EFI_PARTITION=/dev/nvme0n1p1
export BOOT_PARTITION=/dev/nvme0n1p2
# this partition will be the LUKS container, holding the LVM and your Linux install
export PARTITION_FOR_LUKS=/dev/nvme0n1p3
# name of the LVM group we'll create
export VG_NAME=vg0
# name of the LVM volume that will host the system
export OS_VOLUME_NAME=manjaro

Make the chosen partition into a LUKS container:

sudo cryptsetup luksFormat --type luks1 $PARTITION_FOR_LUKS

I’m using luks1 instead of luks2, because the latter isn’t handled by GRUB yet.

Now we need to open the newly created LUKS container (you can use any other name than crypt, of course):

sudo cryptsetup luksOpen $PARTITION_FOR_LUKS crypt

What people usually recommend (e.g. paragraph 2.1.6 from cryptsetup’s FAQ) is to fill the LUKS container with zeroes, so that it looks like random data on the drive, but because that doesn’t seem so dangerous, I’m skipping that step.

Next, mark the opened LUKS container as a “physical volume” for LVM, and create the LVM group:

sudo lvm pvcreate /dev/mapper/crypt
sudo vgcreate $VG_NAME /dev/mapper/crypt

And finally, create the LVM volume that will host your OS. I’ve chosen a size (853 gigabytes) that will leave me 100 gigs for creating a new volume with another Linux install in the future for experiments:

sudo lvcreate -L 853G -n $OS_VOLUME_NAME $VG_NAME

Now, lsblk (for me) reports this layout:

nvme0n1           259:0    0 953.9G  0 disk
├─nvme0n1p1       259:4    0   200M  0 part
├─nvme0n1p2       259:5    0   512M  0 part
└─nvme0n1p3       259:6    0 953.2G  0 part
  └─crypt         254:0    0 953.2G  0 crypt
    └─vg0-manjaro 254:1    0   853G  0 lvm

Restoring the old partitions on the new drive

Now, cd into the place where you’ve stored the partition images, and copy them over to the new partitions one by one:

sudo dd if=efi_partition_image.bin of=$EFI_PARTITION bs=8M status=progress
sudo dd if=boot_partition_image.bin of=$BOOT_PARTITION bs=8M status=progress
sudo dd if=root_partition_image.bin of=${OS_VOLUME_PATH} bs=8M status=progress

In my case, the root partition has more space than it had on the previous drive. Because a filesystem retains its size when copied over with dd, it won’t be making use of that additional space. That’s how you expand the (ext4) filesystem so that it takes all the space available in the volume:

sudo resize2fs ${OS_VOLUME_PATH}

If for the EFI and boot partitions you’ve also allocated more space than they had on the previous drive, you can enlarge their filesystems accordingly:

sudo resize2fs $EFI_PARTITION
sudo resize2fs $BOOT_PARTITION

Chrooting into the old Linux install

If you’d reboot the system now and tried booting from the EFI partition, you’d fail. We still need to adjust some files.

To do that, we first need to mount the partitions we’ve created for the live Linux we’re working in:

sudo mount $OS_VOLUME_PATH /mnt
sudo mount $BOOT_PARTITION /mnt/boot
sudo mount $EFI_PARTITION /mnt/boot/efi

You’ll be able to browse your old files in /mnt right now.

Next you need to bind-mount some pseudo-directories:

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

Now, everything’s prepared for using chroot to “get inside” that old install:

sudo chroot /mnt

You should now have a root shell running in your old Linux system.

Modifying the “tab” files

Now that you’re chrooted into your old Linux install, we need to fixup a few things in order to make it bootable.

First, run blkid command to get the UUID of the partition hosting your LUKS container. For me, the output looks like this:

/dev/loop1: TYPE="squashfs"
/dev/mapper/vg0-manjaro: UUID="e980c99e-acb7-4264-9ed3-300f65694b42" BLOCK_SIZE="4096" TYPE="ext4"
/dev/nvme0n1p3: UUID="050a93bf-d0d3-4d01-83c7-b65d060d2cc5" TYPE="crypto_LUKS" PARTUUID="e18e4927-c79d-4283-a1b9-e2f41cb92a2d"

Because my LUKS container is hosted on /dev/nvme0n1p3, I note the UUID 050a93bf-d0d3-4d01-83c7-b65d060d2cc5. This UUID needs to be added to /etc/crypttab file (you can use nano or vim to edit the files), to instruct the booting system to open the container. The line in the file will look like this:

crypt UUID=050a93bf-d0d3-4d01-83c7-b65d060d2cc5 none luks

As previously, I’m using crypt as the name under which the unencrypted partition will appear.

Now, let’s edit /etc/fstab. Because the UUIDs of all the partitions are copied over from the images you might not need to do that, but I wanted the root filesystem (/) mount to clearly point to the LVM volume containing the Linux install (/dev/vg0/manjaro). My full fstab looks like this:

UUID=7E5B-9C2C                            /boot/efi      vfat    defaults,noatime 0 2
UUID=4f3c8672-650d-4a8b-9697-1817ec53bb78 /boot          ext4    defaults,noatime,discard 0 2
/dev/vg0/manjaro                          /              ext4    defaults,noatime,discard 0 1
tmpfs                                     /tmp           tmpfs   defaults,noatime,mode=1777 0 0
/swapfile                                 none           swap    defaults 0 0

Rebuilding the initial RAM disk and GRUB

We need to make sure that the initial RAM disk that bootstraps your system during boot can work with LUKS and LVM. So you need to add lvm2 and encrypt modules to the HOOKS variable in /etc/mkinitcpio.conf (might be a different place in your distro). I saw advice saying they should be after keyboard and before filesystems. That’s how the variable looks for me:

HOOKS="base udev autodetect modconf block keyboard keymap encrypt lvm2 filesystems"

Next, add a cryptdevice instruction pointing to your LUKS partition (should be the same UUID as in your crypttab), to GRUB_CMDLINE_LINUX_DEFAULT in /etc/default/grub. On my system (notice other parameters mindlessly stolen from a default encrypted Manjaro install):

GRUB_CMDLINE_LINUX_DEFAULT="cryptdevice=UUID=050a93bf-d0d3-4d01-83c7-b65d060d2cc5:crypt apparmor=1 security=apparmor udev.log_priority=3"

Now, run this (or the equivalent for your distribution):

mkinitcpio -P

Something that might be needed so that GRUB can work with EFI [8]:

mount -t efivarfs efivarfs /sys/firmware/efi/efivars

Prepare the GRUB config:

# depending on your distro, this command can be different, e.g. `update-grub`
grub-mkconfig -o /boot/grub/grub.cfg

For me, it gives this output:

Generating grub configuration file ...
Found theme: /usr/share/grub/themes/manjaro/theme.txt
Found linux image: /boot/vmlinuz-5.4-x86_64
Found initrd image: /boot/amd-ucode.img /boot/initramfs-5.4-x86_64.img
Found initrd fallback image: /boot/initramfs-5.4-x86_64-fallback.img
Warning: os-prober will be executed to detect other bootable partitions.
Its output will be used to detect bootable binaries on them and create new boot entries.
grub-probe: error: cannot find a GRUB drive for /dev/sdb1.  Check your
grub-probe: error: cannot find a GRUB drive for /dev/sdb1.  Check your
Adding boot menu entry for UEFI Firmware Settings ...
Found memtest86+ image: /boot/memtest86+/memtest.bin

Notice that error with /dev/sdb1 which is the previous location of one of the partitions. I can’t figure out how to fix it or how to “check my”, but that doesn’t seem to be affecting anything.

And now, the final step - install GRUB to the EFI partition:

# the actual partition might be different for you, of course
grub-install /dev/nvme0n1p1

My output:

Installing for x86_64-efi platform.
Installation finished. No error reported.

And that’s it! The system should be ready to go.

Now reboot your computer. You should see GRUB, after picking your OS you will be asked for the passphrase for your LUKS container, and after that your old system should boot normally.



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