To copy the root fs, ssh into the machine and log in as root (sudo -i). Next, make the file system read only.
# echo u > /proc/sysrq-triggerTo verify, this took, you can run touch file, and you should get the following.
touch: cannot touch 'file': Read-only file system
Next, copy the image to your workstation.
dd if=/dev/mmcblk0p1 | ssh [email protected] dd of=/home/you/xavier_image_$(date --iso-8601).raw status=progress
Then grab a cup of coffee, because that will take a while.
To flash the image, grab the CTI and extract following their instructions.
After extraction, you need to generate the system.img file to flash using the raw image we took of the filesystem.
cd ~/nvidia/nvidia_sdk/JetPack_Version_Linux_JETSON_AGX_XAVIER/Linux_for_Tegra/bootloader
sudo ./mksparse -v ~/xavier_image.raw system.img
replacing Version with the correct jetpack (e.g. 4.5.1), and xavier_image.raw with the image taken above.
cd ~/nvidia/nvidia_sdk/JetPack_Version_Linux_JETSON_AGX_XAVIER/Linux_for_Tegra
sudo ./flash.sh -r cti/xavier/rogue mmcblk0p1