Debian – Prevent Debian from auto-assembling RAID at boot

fdisk is the wrong tool for disks >2TB. Use parted or gdisk instead.

It appears that /dev/sdc1 and /dev/sdd1 are 2TB partitions, so that's what limits your array size. For the other disks, they have GPT so I assume they are 3TB already, but you should check.

Basically you have to stop the array, enlarge each partition to 3TB (without changing the starting offset), then start it again and follow it up with a grow:

mdadm --grow /dev/md0 --size=max

If you can't stop the array, you'll have to fail each 2TB partition individually, repartition and re-add it. This might go faster if you add a write-intent bitmap first.

mdadm --grow /dev/md0 --bitmap=internal

Then for each disk individually,

mdadm /dev/md0 --fail /dev/disk1 # check mdstat for [UUUU] first
mdadm /dev/md0 --remove /dev/disk1
parted /dev/disk -- mklabel gpt mkpart primary 1mib -1mib
mdadm /dev/md0 --re-add /dev/disk1
mdadm --wait /dev/md0 # must wait for sync

Once that's done you can remove the bitmap again (keeping it may harm performance).

mdadm --grow /dev/md0 --bitmap=none
mdadm --grow /dev/md0 --size=max

Finally do your resize2fs or whatever.

It's not actually grub which does this, but the initramfs. On Debian, the default initramfs implementation is the one inside the initramfs-tools package. What your initramfs does exactly to be able to mount the root filesystem can depend on many factors, including things like which packages are installed (packages can add hook scripts to extend the initramfs functionality) at the time when update-initramfs was last called, and how they were configured.

Since the problem appears to be that your mdraid devices aren't being rebuilt, I suspect that your mdadm package hasn't been configured right. Try to fix that first:

sudo dpkg-reconfigure mdadm

After that, the initramfs should be updated automatically.

If that doesn't fix it, and as part of your migration to software RAID you created a new filesystem, then it may be that your fstab has the UUID of the old filesystem, which now no longer matches the new filesystem. Check this:

grep $(blkid /dev/md0) /etc/fstab

If that produces no output, then edit /etc/fstab to replace the UUID specified there for the root device with the output of blkid /dev/md0, and run update-initramfs again.