It's hard to edit partition table in virtual machine when host thinks that sectors are 4k and vm thinks they are 512 bytes. fdisk --sector-size 512 doesn't seem to work, so only solution is to boot something inside vm to produce original hardware configuration. cd /boot wget http://download.grml.org/grml96-small_2017.05.iso root@r1u28:/home/dpavlin# gnt-cluster copyfile /boot/grml96-small_2017.05.iso # force boot from cdrom root@r1u28:/home/dpavlin# gnt-instance modify -H kernel_path=,initrd_path=,boot_order=cdrom,cdrom_image_path=/boot/grml96-small_2017.05.iso armbian # reboot, connect with vnc and fix system root@r1u28:/home/dpavlin# gnt-instance reboot armbian root@r1u28:/home/dpavlin# /srv/gnt-info/gnt-vnc.sh armbian ssh -L 11032:127.0.0.1:11032 r1u30.gnt.ffzg.hr vncviewer localhost:5132 # remove cdrom, restore boot from disk root@r1u28:/home/dpavlin# gnt-instance modify -H kernel_path=,initrd_path=,boot_order=disk,cdrom_image_path= armbian # restore kernel root@r1u28:/home/dpavlin# gnt-instance modify -H initrd_path=/boot/initrd.img-4.9.0-0.bpo.6-amd64,kernel_path=/boot/vmlinuz-4.9.0-0.bpo.6-amd64 armbian