First of all you need to install the toolchain (cross compiler, linker, etc) on your Linux Ubuntu PC following this article (tested on Ubuntu 18.04.4 LTS):
wget https://github.com/linux4sam/at91bootstrap/archive/refs/tags/v4.0.4.zip
unzip v4.0.4.zip
cd at91bootstrap-4.0.4
wget https://www.acmesystems.it/www/at91bootstrap_4_0_4/acme.patch
patch -p1 < acme.patch
Roadrunner
make roadrunner_defconfig
Acqua
make acqua_defconfig
To compile at91bootstrap type:
make CROSS_COMPILE=arm-linux-gnueabihf-
it will generate a binary file in build/binaries directory called __boot.bin_.
Insert a microSD on your Linux PC and type:
cp build/binaries/boot.bin /media/$USER/boot
Be sure that PA30 (MMC1 CD) is wired on GND.