Monday, 8 November 2021

Clone the Raspberry boot disk

Updated 2021-11-08 !

A very nice way to fix a backup is to make a copy, bootable, of the actual SD card You are using on the Raspberry Pi(RPi). This will be done even when the RPi is up and running !

This application can also be used to make a bootable SSD or USB drive !!

You clone from the command line so You don't need the standard GUI, Pixel, and the "SD card copier
" function.

It is also possible to set up a a scheduled job, cronjob explained later, which for example makes a clone every night at 1 o'clock.

Check SD
You just need a USB SD card reader, with a SD Card, and then You plug the SD Card reader into a free USB port on the RPi.

Log on to the RPi and at a command line type


Which checks if the SD Card is "accepted" and also which name it's assigned to. Could be "sda", "sdb" ......

Then download the scripts from Github where You also can find additional info about the scripts. For example the scripts handles that You are cloning from/to SD Cards with different sizes.

Install with GIT
If You haven't used GitHub before You have to download an additional software with

sudo apt-get install git

and then download the actual scripts

git clone

Install without GIT

Unzip and rename 

unzip && mv rpi-clone-master rpi-clone

Common commands
Copy the scripts to the folder used for scripts with superuser (root) privileges.

sudo cp rpi-clone/rpi-clone* /usr/local/sbin

Clean up, deleting the working folders

rm -rf rpi-clone

Manual clone 
Execute the clone script with 

sudo bash rpi-clone sda -f

(The USB could be assigned another name than "sda", so use the name You got earlier) and something like this will appear

Booted disk: mmcblk0 15.9GB                Destination disk: sda 15.9GB
Part      Size    FS     Label           Part   Size    FS     Label
1 /boot   43.5MB  fat32  --              1      43.5MB  fat32  --
2 root    15.9GB  ext4   cpy_stretch     2      15.9GB  ext4   --
== Initialize: IMAGE mmcblk0 partition table to sda - forced by option ==
1 /boot               (21.5MB used)  : IMAGE     to sda1  FSCK
2 root                (2.0GB used)   : RESIZE(15.9GB) MKFS SYNC to sda2
Run setup script       : no
Verbose mode           : no
** WARNING **          : All destination disk sda data will be overwritten!
                       :   The partition structure will be imaged from mmcblk0.
Initialize and clone to the destination disk sda?  (yes/no):

Answer with yes and type a label for the destination SD card

Optional destination  ext type file system label (16 chars max): XX
  Imaging past the start of /boot partition 2.
  => dd if=/dev/mmcblk0 of=/dev/sda bs=1M count=50 ...
  Resizing last partition to end of disk ...
    Resize success.
  Changing destination Disk ID ...
  Delaying so partprobe can update /dev entries ...
  => fsck -p /dev/sda1 ...
  => mkfs -t ext4 -L XX /dev/sda2 ...
Syncing file systems (can take a long time)
Syncing mounted partitions:
  Mounting /dev/sda2 on /mnt/clone
  => rsync // /mnt/clone with-root-excludes ...
  Mounting /dev/sda1 on /mnt/clone/boot
  => rsync /boot/ /mnt/clone/boot  ...
Editing /mnt/clone/boot/cmdline.txt PARTUUID to use dee316b8
Editing /mnt/clone/etc/fstab PARTUUID to use dee316b8
Done with clone to /dev/sda
   Start - 12:06:06    End - 12:12:36    Elapsed Time - 6:30
Cloned partitions are mounted on /mnt/clone for inspection or customizing.
Hit Enter when ready to unmount the /dev/sda partitions ...
  unmounting /mnt/clone/boot
  unmounting /mnt/clone

In this case I cloned from/to 16 Gb SD Card with approx 2 Gb of data.

Before you hit "Enter", to unmount, the destination can be checked with 

ls -la  /mnt/clone

Automated clone
To add an automated setup, from a command line, type

crontab -e

If it's the first cronjob You are adding, something like this will appear

no crontab for pi - using an empty one
Select an editor.  To change later, run 'select-editor'.
  1. /bin/ed
  2. /bin/nano        <---- easiest
  3. /usr/bin/vim.tiny
Choose 1-3 [2]: 
crontab: installing new crontab

where You select the editor You want to use.

On the last line add 

0 1 * * * sudo bash rpi-clone sda -q

and exit. This means that a new clone will be made every night at 1 o'clock

Clone alternative

Use the standard "Accessories => CD Card Copier" found in the RPi meny. (If you don't use RPi OS lite) 
If not installed ? sudo apt install piclone


  1. Wonderful, it´s just what I was looking for. Thanks a lot!

  2. Thank you so much! Other tutorials were too complicated, this one is the easiest and the greatest! I'm working on a project and I don't want to lose my data after corruption so going to copy the whole OS onto another SD card.

  3. Nice!
    I am doing a copy of the SD card before I do changes and I am always using
    SD Card Copier in Raspian. Never failed so far :-)

    1. Thanks, but if You are using Raspbian Lite, without GUI, You can't use SD Card Copier, or ?

    2. Sorry did not think of that :-( My mistake!

    3. No problem.... just so I got it right ;-)

  4. Hi and thanks for your tuto!
    I have a question, my RPi4 boot with part boot on sdcard and after, the rootfs part is on a SSD.I'm waiting for native boot on RPi4 ;)
    So today may it possible to use RPI Clone to clone my rootfs to a sdcard.
    My rootfs is about 15Gb on my SSD and my SDcard is a 64Gb.

    1. Good question, but sorry to say I don't have any answer. Think the best way is to open an issue on GitHub.

  5. On the line "Optional destination ext type file system label (16 chars max): XX", did you enter "XX" so it knows it's a bootable card? I entered something different and my card won't boot.

    1. It's just a label so it will not affect the boot process. Corrupt SD card ?

  6. Pi4 - I have successully made an SD of the new Raspbian that works both as SD and USB for USB boot and I've used rpi-clone to make a copy to a real USB which also boots.. I need to get back my working setup of a slightly older SD which will NOT USB boot. Can I somehow use pi-clone ONLY to overwite the second partition to make a new USB boot compatibe version of my workingg installation? Any ideas?

    1. Good question. I'm not the author of the script and I see that You already created an issue on GitHub, which was my recommendation for "next step".

  7. Great! I followed this post step by step and it works flawlessy.
    Thanx for this info!
    When I make the cronjob, it will be saved with an not easy readable name.
    It is saved in the "tmp" directory, which is not accessable.
    Edit with crontab-e
    Can I save it with an more readable name?

    1. Thanks ! Don't bother about the filename it's just a temporary one before the changed info is stored in the "/usr/bin/crontab" file.

  8. Strange things hapen ;-). Think with me plse.
    • Rpi3B+ regular running on a 16Gb stick => call it: “operation stick A”
    • Back up SSD (yes indeed the same Kingspec) => call it: SSD KS.

    • Back up method: Pyssel.

    • First manual Back-up: January 26.
    • Cronjob back up: every night at 3 o’clock.

    • Test: January 29.
    • Remove: Rpi “operation stick A “
    • Start up with only SSD KS => OK, including actual data past 24 houre.

    • Start up with only “operation stick A “ => OK, BUT NO actual data past 24 houre.

    • This means the Rpi is not running on the “operation stick A” but is running on the Back up SSD KS???

    Any idea how/what?

    Thnx, Thomas

  9. My fault ;-(
    Found myself the solution due to my numeration in my post herefore ;-)
    I have set the wrong sd* usb port.
    Useful command to asure you select the right usb ports:


  10. To avoid any doubt. In the cronjob you specify the destination disk. You back up here To and not From. (correct me if i'am wrong.
    (thanks for your patience)

    1. Correct. Using "lsblk -f" as said in the beginning of this post you will get the target/destination name. And in that respect there is no differens using the command at a command line or in a cronjob.

  11. I have been trying for days to find a good way to make a backup image of my Octopi image on my raspberry pi. This is the BEST and clearest instructions on exactly what to do. I used Putty to log into my pi and enter the recommended commands. Thanks a million

  12. As a side note, while this guide was excellent in every respect, I had one bit of trouble... Yes, in hindsight, I should have been able to catch it, but... This wouldn't boot to my ssd attached until I edited /etc/fstab.
    I used this to copy an image from microsdcard to M.2 Sata, as I was unable to simply burn to the M.2... Wouldn't complete boot, hung after the message random: crng initdone...

    Using this most Excellent guide, I was able to make an exact copy of a bootable sd card to my preferred usb booting method using the M.2.

    Just a note if someone has issues... it's easy to overlook.

  13. Hi Pyssel, for the /etc/fstab I also needed to change something.
    First when booted with sdcard and the SSD connected I found out the PARTUUID with: ls -l /dev/disk/by-partuuid
    Then I put that ID in place of what was already there in the fstab file.
    Then shutdown pi and reboot. Now it boots from the SSD correctly :)

    1. Hi and thanks for the feedback. Never had the problem myself but hope that your comment will help others with similar problem.