Notes about open source software, computers, other stuff.

Tag: storage

Telling update-grub to ignore my ZFS backups

As I was running some manual package upgrades on my Ubuntu 24.04 server, I noticed that a kernel upgrade led to a long series of kernels being listed. This was strange, as there should have been only two or three. Closer inspection revealed that the update-grub command tries to find all kernels and also looks for kernels on ZFS datasets. Given that I extensively use ZFS, I was aware of that, and normally this is the behaviour I want.

However, in this case, my home server doesn’t have root on ZFS, but on a regular MD RAID mirror with LVM. Looking at the kernels listed during the upgrade, I noticed that update-grub was digging through all ZFS datasets and their snapshots on the server, including the backups sent to my home server from various other machines, some of which do have root on ZFS. All in all this led to a huge list of kernels and a kernel upgrade process that never seemed to end.

A quick web search pointed me to this AskUbuntu.com answer, which showed that the ZFS parsing code can be found in /etc/grub.d/10_linux_zfs. In there, I found the following code block (note, for improved readability I split the long command above the done over multiple lines and added corresponding \):

# List all the dataset with a root mountpoint
get_root_datasets() {
    local pools="$(zpool list | awk '{if (NR>1) print $1}')"

    for p in ${pools}; do
        local rel_pool_root=$(zpool get -H altroot ${p} | awk '{print $3}')
        if [ "${rel_pool_root}" = "-" ]; then
            rel_pool_root="/"
        fi

        zfs list -H -o name,canmount,mountpoint -t filesystem | \
            grep -E '^'"${p}"'(\s|/[[:print:]]*\s)(on|noauto)\s'"${rel_pool_root}"'$' | \
            awk '{print $1}'
    done
}

This function first lists all the ZFS pools on the system and then (with the last, long command above the done), for each of those, returns the filesystem datasets that can be mounted.

The solution was simple: because all backups from external systems end up as datasets below the remote_backups dataset on my storage pool, simply changed the last awk statement so that it only prints datasets that don’t match remote_backups by adding $1 !~ "remote_backups":

zfs list -H -o name,canmount,mountpoint -t filesystem | \
    grep -E '^'"${p}"'(\s|/[[:print:]]*\s)(on|noauto)\s'"${rel_pool_root}"'$' | \
    awk '$1 !~ "remote_backups" {print $1}'

This way, the code would still work if I ever move this system to have root on ZFS, but now update-grub skips all backups and finds only the kernels relevant for my home server :-).

Related Images:

Expanding a partition-backed ZFS special device

The spinning disk pool on my home server uses a mirrored special device (for storing metadata and small blocks, see also this blog post at Klara Systems) based on two NVMe SSDs. Because my home server only has two M.2 slots and I wanted to have a pure SSD ZFS pool as well, I partitioned the SSDs. Each SSD has a partition for the SSD pool and one for the special device of the storage pool (which uses a mirror of spinning disks).

Note: This isn’t really a recommended production setup as you are basically hurting performance of both the special device and the SSD pool. But for my home server this works fine. For example, I use the special device’s small blocks functionality to store previews of the photo’s I store on my Nextcloud server. This makes scrolling through the Memories app’s timeline a breeze, even though the full-size photo’s are stored on the spinning disks.

Today, I noticed that the special device had filled up, and, given that there was still some unpartitioned space on the SSDs, I wondered if I could just expand the partition (using parted) used by the special device and then have the ZFS pool recognise the extra space. In the past I have expanded partition-based ZFS pools before, e.g. on after upgrading the SSD on my laptop, but I hadn’t tried this with a special device before.

After some experimentation, I can tell you: this works.

Here is how I tested this on a throw-away file-backed zpool. First create four test files: two for the actual mirror pool and two that I’ll add as a special device.

for i in {0..3} ; do truncate -s 1G file$i.raw ; done
ls -lh
total 4,0K
-rw-rw-r-- 1 lennart lennart 1,0G mrt 11 12:46 file0.raw
-rw-rw-r-- 1 lennart lennart 1,0G mrt 11 12:46 file1.raw
-rw-rw-r-- 1 lennart lennart 1,0G mrt 11 12:46 file2.raw
-rw-rw-r-- 1 lennart lennart 1,0G mrt 11 12:46 file3.raw

Create a regular mirror pool:

zpool create testpool mirror $(pwd)/file0.raw $(pwd)/file1.raw
zpool list -v testpool
NAME                       SIZE  ALLOC   FREE  CKPOINT  EXPANDSZ   FRAG    CAP  DEDUP    HEALTH  ALTROOT
testpool                   960M   146K   960M        -         -     0%     0%  1.00x    ONLINE  -
  mirror-0                 960M   104K   960M        -         -     0%  0.01%      -    ONLINE
    /tmp/tests/file0.raw     1G      -      -        -         -      -      -      -    ONLINE
    /tmp/tests/file1.raw     1G      -      -        -         -      -      -      -    ONLINE

Add the special device to the zpool:

zpool add testpool special mirror $(pwd)/file2.raw $(pwd)/file3.raw
zpool list -v testpool
NAME                       SIZE  ALLOC   FREE  CKPOINT  EXPANDSZ   FRAG    CAP  DEDUP    HEALTH  ALTROOT
testpool                  1.88G   190K  1.87G        -         -     0%     0%  1.00x    ONLINE  -
  mirror-0                 960M   190K   960M        -         -     0%  0.01%      -    ONLINE
    /tmp/tests/file0.raw     1G      -      -        -         -      -      -      -    ONLINE
    /tmp/tests/file1.raw     1G      -      -        -         -      -      -      -    ONLINE
special                       -      -      -        -         -      -      -      -         -
  mirror-1                 960M      0   960M        -         -     0%  0.00%      -    ONLINE
    /tmp/tests/file2.raw     1G      -      -        -         -      -      -      -    ONLINE
    /tmp/tests/file3.raw     1G      -      -        -         -      -      -      -    ONLINE

I wasn’t sure whether I could just truncate the backing files for the special device to a larger size while they were part of the pool, so I detached them one by one and created new ones of 2GB, and then reattached them:

zpool detach testpool /tmp/tests/file2.raw
zpool list -v testpool
truncate -s 2G file2.raw
zpool attach testpool $(pwd)/file3.raw /tmp/tests/file2.raw
zpool list -v testpool

NAME                       SIZE  ALLOC   FREE  CKPOINT  EXPANDSZ   FRAG    CAP  DEDUP    HEALTH  ALTROOT
testpool                  1.88G   194K  1.87G        -         -     0%     0%  1.00x    ONLINE  -
  mirror-0                 960M   104K   960M        -         -     0%  0.01%      -    ONLINE
    /tmp/tests/file0.raw     1G      -      -        -         -      -      -      -    ONLINE
    /tmp/tests/file1.raw     1G      -      -        -         -      -      -      -    ONLINE
special                       -      -      -        -         -      -      -      -         -
  /tmp/tests/file3.raw       1G    90K   960M        -         -     0%  0.00%      -    ONLINE
NAME                       SIZE  ALLOC   FREE  CKPOINT  EXPANDSZ   FRAG    CAP  DEDUP    HEALTH  ALTROOT
testpool                  1.88G   278K  1.87G        -         -     0%     0%  1.00x    ONLINE  -
  mirror-0                 960M  97.5K   960M        -         -     0%  0.00%      -    ONLINE
    /tmp/tests/file0.raw     1G      -      -        -         -      -      -      -    ONLINE
    /tmp/tests/file1.raw     1G      -      -        -         -      -      -      -    ONLINE
special                       -      -      -        -         -      -      -      -         -
  mirror-1                 960M   180K   960M        -         -     0%  0.01%      -    ONLINE
    /tmp/tests/file3.raw     1G      -      -        -         -      -      -      -    ONLINE
    /tmp/tests/file2.raw     2G      -      -        -         -      -      -      -    ONLINE

And for the second “disk”:

zpool detach testpool /tmp/tests/file3.raw
zpool list -v testpool
truncate -s 2G file3.raw
zpool attach testpool $(pwd)/file2.raw /tmp/tests/file3.raw
zpool list -v testpool

NAME                       SIZE  ALLOC   FREE  CKPOINT  EXPANDSZ   FRAG    CAP  DEDUP    HEALTH  ALTROOT
testpool                  1.88G   218K  1.87G        -         -     0%     0%  1.00x    ONLINE  -
  mirror-0                 960M    66K   960M        -         -     0%  0.00%      -    ONLINE
    /tmp/tests/file0.raw     1G      -      -        -         -      -      -      -    ONLINE
    /tmp/tests/file1.raw     1G      -      -        -         -      -      -      -    ONLINE
special                       -      -      -        -         -      -      -      -         -
  /tmp/tests/file2.raw       2G   152K   960M        -        1G     0%  0.01%      -    ONLINE
NAME                       SIZE  ALLOC   FREE  CKPOINT  EXPANDSZ   FRAG    CAP  DEDUP    HEALTH  ALTROOT
testpool                  1.88G   296K  1.87G        -         -     0%     0%  1.00x    ONLINE  -
  mirror-0                 960M    54K   960M        -         -     0%  0.00%      -    ONLINE
    /tmp/tests/file0.raw     1G      -      -        -         -      -      -      -    ONLINE
    /tmp/tests/file1.raw     1G      -      -        -         -      -      -      -    ONLINE
special                       -      -      -        -         -      -      -      -         -
  mirror-1                 960M   242K   960M        -        1G     0%  0.02%      -    ONLINE
    /tmp/tests/file2.raw     2G      -      -        -        1G      -      -      -    ONLINE
    /tmp/tests/file3.raw     2G      -      -        -         -      -      -      -    ONLINE

And now, here comes the magic. Time to expand the pool and see of the special device will grow to 2GB:

zpool online -e testpool $(pwd)/file2.raw $(pwd)/file3.raw
zpool list -v testpool
NAME                       SIZE  ALLOC   FREE  CKPOINT  EXPANDSZ   FRAG    CAP  DEDUP    HEALTH  ALTROOT
testpool                  2.88G   226K  2.87G        -         -     0%     0%  1.00x    ONLINE  -
  mirror-0                 960M    48K   960M        -         -     0%  0.00%      -    ONLINE
    /tmp/tests/file0.raw     1G      -      -        -         -      -      -      -    ONLINE
    /tmp/tests/file1.raw     1G      -      -        -         -      -      -      -    ONLINE
special                       -      -      -        -         -      -      -      -         -
  mirror-1                1.94G   178K  1.94G        -         -     0%  0.00%      -    ONLINE
    /tmp/tests/file2.raw     2G      -      -        -         -      -      -      -    ONLINE
    /tmp/tests/file3.raw     2G      -      -        -         -      -      -      -    ONLINE

Yay! It worked! So, for my actual storage pool, I ended up doing the following:

  • Given that the partitions used by the special device are located at the end of the SSD, it was easy to expand them using parted resizepart.
  • Run zpool online -e storage partname-1 partname-2 (so I didn’t detach/attach here).

Don’t forget to clean up the testpool:

zpool destroy testpool
rm -r /tmp/tests

Related Images:

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