clone root partition via rsync (to handle 512 vs 4k sector size)

my root partition is failing, giving random io errors during boot. it's a 5 year old 180G hdd using 512 byte sectors. the modern replacement is a 1TB hdd with 4096 byte sectors. so a straight up dd isn't an option. need to do a file by file copy instead mount /dev/sdc1 /mnt # -x limits rsync to a single partition rsync -avxHSAX / /mnt/ for ii in /dev /dev/pts /proc /sys /run; do sudo mount -B $ii /mnt$ii; done sudo chroot /mnt grub-install --recheck /dev/sdc update-grub # label the partition for use in fstab e2label /dev/sdc1 mylabel blkid -c /dev/null gedit /mnt/etc/fstab the error messages are somewhat cryptic. from syslog: ata2.00: exception Emask 0x0 SAct 0x4 SErr 0x0 action 0x0 ata2.00: irq_stat 0x40000008 ata2.00: failed command: READ FPDMA QUEUED ata2.00: cmd 60/08:10:d7:00:19/00:00:0b:00:00/40 tag 2 ncq 4096 in res 51/40:08:d7:00:19/00:00:0b:00:00/40 Emask 0x409 (media error) ata2.00: status: { DRDY ERR } ata2.00: error: { UNC } ata2.00: configured for UDMA/133 sd 1:0:0:0: [sda] Unhandled sense code sd 1:0:0:0: [sda] Result: hostbyte=DID_OK driverbyte=DRIVER_SENSE sd 1:0:0:0: [sda] Sense Key : Medium Error [current] [descriptor] Descriptor sense data with sense descriptors (in hex): 72 03 11 04 00 00 00 0c 00 0a 80 00 00 00 00 00 0b 19 00 d7 sd 1:0:0:0: [sda] Add. Sense: Unrecovered read error - auto reallocate failed sd 1:0:0:0: [sda] CDB: Read(10): 28 00 0b 19 00 d7 00 00 08 00 end_request: I/O error, dev sda, sector 186187991 ata2: EH complete and fsck shows some errors, eg "Attempt to read block from filesystem resulted in short read" and some unattached inodes
using rsync to clone
installing grub via chroot