Clone the Raspberry boot disk

Updated 2024-02-20 !

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

lsblk

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

On Github You can find additional info about the application. For example it handles that You are cloning from/to SD Cards with different sizes.

Install
Run the script

curl https://raw.githubusercontent.com/geerlingguy/rpi-clone/master/install | sudo bash

If you would like to run installation manually check here.

Manual clone 
Execute the clone script with 

sudo 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
Initializing
  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, in another terminal window, 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

With GUI installed 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

Remark 

On one of my RPi 4 I suddenly couldn't boot from SD-card and got the message, on the monitor, 

Failed to open device: ’sdcard’ (cmd 371a0010 status 1fff0001)

Googled a little and found that this could happen when the SD card slot broken. So how to fix it ? 

I could do some soldering and exchange the broken slot but bought a fast USB 3 flash drive, cloned the SD card to the flash drive, inserted it in one of USB 3 ports and booted from that instead.