Wrong space summary in the GUI after docker prune

Hi, I recently saw that the pool of my apps is way more used than it should. After some digging, I found out that the issue was that I had almost 150GB of unused docker images sitting in the .ix-apps inside /mnt. When I made some cleanup with docker image prune and docker system prune, the du command no longer shows a huge .ix-apps data usage, as it should be, but the GUI and the command zpool list still shows the usage as being the same as before.

Here are some informations :

Running Truenas Scale 24.10.2. I have 3 pools : Piscine, Safe and FastBoy. FastBoy is the app pool and also the problematic one.

Here are the outputs of cmds :

root@truenas:/# zpool list
NAME        SIZE  ALLOC   FREE  CKPOINT  EXPANDSZ   FRAG    CAP  DEDUP    HEALTH  ALTROOT
FastBoy     446G   253G   193G        -         -    18%    56%  1.00x    ONLINE  /mnt
Piscine    1.81T  1.12T   709G        -         -    17%    61%  1.00x    ONLINE  /mnt
Safe       2.72T   216G  2.51T        -         -    14%     7%  1.00x    ONLINE  /mnt
boot-pool    95G  19.9G  75.1G        -         -    10%    20%  1.00x    ONLINE  -
du -d 2 -h | sort -h

[...]

174M    ./boot
316M    ./usr/bin
688M    ./usr/share
1.3G    ./usr/lib
2.3G    ./var/db
2.4G    ./var
2.5G    ./usr
39G     ./mnt/FastBoy
66G     ./mnt/.ix-apps
76G     ./mnt/Safe
1.1T    ./mnt/Piscine
1.3T    .
1.3T    ./mnt

I dont really understand the difference in sizes and why it dit not update. I also checked the snapshots and dont seem to have any that use more than 3GB.

How can I fix this issue ? Thanks a lot.

Try running sudo du instead.

Du recurses filesystem and calculates based on files located there. It won’t show space consumed by snapshots for instance.

zfs list -o space gives better view of how space is used.

Thank you for your response, here is the result of that command :

FastBoy                                                                         108G   324G        0B     96K             0B       324G
FastBoy/GitlabRunnerSSD-qjyli                                                   159G  63.1G     4.12G   8.45G          50.6G         0B
FastBoy/Ubuntu_Server_24-bszycc_LanguageTool                                    108G  46.4G     20.9G   25.6G             0B         0B
FastBoy/ix-applications                                                         108G  38.3G        0B   4.12M             0B      38.3G
FastBoy/ix-applications/catalogs                                                108G  48.7M       24K   48.6M             0B         0B
FastBoy/ix-applications/default_volumes                                         108G    96K        0B     96K             0B         0B
FastBoy/ix-applications/k3s                                                     108G  38.2G        0B   38.2G             0B       352K
FastBoy/ix-applications/k3s/kubelet                                             108G   352K        0B    352K             0B         0B
FastBoy/ix-applications/releases                                                108G  10.4M        0B    136K             0B      10.3M
FastBoy/ix-applications/releases/collabora                                      108G  1.75M        0B    104K             0B      1.65M
FastBoy/ix-applications/releases/collabora/charts                               108G  1.46M        0B   1.46M             0B         0B
FastBoy/ix-applications/releases/collabora/volumes                              108G   192K        0B     96K             0B        96K
FastBoy/ix-applications/releases/collabora/volumes/ix_volumes                   108G    96K        0B     96K             0B         0B
FastBoy/ix-applications/releases/ddns-updater                                   108G  1.96M        0B    104K             0B      1.86M
FastBoy/ix-applications/releases/ddns-updater/charts                            108G  1.67M        0B   1.67M             0B         0B
FastBoy/ix-applications/releases/ddns-updater/volumes                           108G   192K        0B     96K             0B        96K
FastBoy/ix-applications/releases/ddns-updater/volumes/ix_volumes                108G    96K        0B     96K             0B         0B
FastBoy/ix-applications/releases/ddns-updater/volumes/ix_volumes/data           108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/elastic-search                                 108G   680K        0B    104K             0B       576K
FastBoy/ix-applications/releases/elastic-search/charts                          108G   376K        0B    376K             0B         0B
FastBoy/ix-applications/releases/elastic-search/volumes                         108G   200K        0B     96K             0B       104K
FastBoy/ix-applications/releases/elastic-search/volumes/ix_volumes              108G   104K        0B     96K             0B         8K
FastBoy/ix-applications/releases/elastic-search/volumes/ix_volumes/data         108G     8K        0B      8K             0B         0B
FastBoy/ix-applications/releases/gitea                                          108G   860K        0B    104K             0B       756K
FastBoy/ix-applications/releases/gitea/charts                                   108G   548K        0B    548K             0B         0B
FastBoy/ix-applications/releases/gitea/volumes                                  108G   208K        0B     96K             0B       112K
FastBoy/ix-applications/releases/gitea/volumes/ix_volumes                       108G   112K        0B    112K             0B         0B
FastBoy/ix-applications/releases/gitea/volumes/ix_volumes/config                108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/gitea/volumes/ix_volumes/data                  108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/gitea/volumes/ix_volumes/pgBackup              108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/gitea/volumes/ix_volumes/pgData                108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/nextcloud                                      108G  1.88M        0B    104K             0B      1.78M
FastBoy/ix-applications/releases/nextcloud/charts                               108G  1.58M        0B   1.58M             0B         0B
FastBoy/ix-applications/releases/nextcloud/volumes                              108G   208K        0B     96K             0B       112K
FastBoy/ix-applications/releases/nextcloud/volumes/ix_volumes                   108G   112K        0B    112K             0B         0B
FastBoy/ix-applications/releases/nextcloud/volumes/ix_volumes/data              108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/nextcloud/volumes/ix_volumes/html              108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/nextcloud/volumes/ix_volumes/pgBackup          108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/nextcloud/volumes/ix_volumes/pgData            108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/nginx-proxy-manager                            108G   640K        0B    104K             0B       536K
FastBoy/ix-applications/releases/nginx-proxy-manager/charts                     108G   336K        0B    336K             0B         0B
FastBoy/ix-applications/releases/nginx-proxy-manager/volumes                    108G   200K        0B     96K             0B       104K
FastBoy/ix-applications/releases/nginx-proxy-manager/volumes/ix_volumes         108G   104K        0B     96K             0B         8K
FastBoy/ix-applications/releases/nginx-proxy-manager/volumes/ix_volumes/certs   108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/nginx-proxy-manager/volumes/ix_volumes/data    108G     8K        0B      8K             0B         0B
FastBoy/ix-applications/releases/paperless-ngx                                  108G  1.71M        0B    104K             0B      1.61M
FastBoy/ix-applications/releases/paperless-ngx/charts                           108G  1.40M        0B   1.40M             0B         0B
FastBoy/ix-applications/releases/paperless-ngx/volumes                          108G   216K        0B     96K             0B       120K
FastBoy/ix-applications/releases/paperless-ngx/volumes/ix_volumes               108G   120K        0B    120K             0B         0B
FastBoy/ix-applications/releases/paperless-ngx/volumes/ix_volumes/consume       108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/paperless-ngx/volumes/ix_volumes/data          108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/paperless-ngx/volumes/ix_volumes/media         108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/paperless-ngx/volumes/ix_volumes/pgBackup      108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/paperless-ngx/volumes/ix_volumes/pgData        108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/paperless-ngx/volumes/ix_volumes/trash         108G     0B        0B      0B             0B         0B
FastBoy/ix-applications/releases/wg-easy                                        108G   844K        0B    104K             0B       740K
FastBoy/ix-applications/releases/wg-easy/charts                                 108G   548K        0B    548K             0B         0B
FastBoy/ix-applications/releases/wg-easy/volumes                                108G   192K        0B     96K             0B        96K
FastBoy/ix-applications/releases/wg-easy/volumes/ix_volumes                     108G    96K        0B     96K             0B         0B
FastBoy/ix-applications/releases/wg-easy/volumes/ix_volumes/config              108G     0B        0B      0B             0B         0B
FastBoy/ix-apps                                                                 108G   176G      756K    140K             0B       176G
FastBoy/ix-apps/app_configs                                                     108G  93.8M     2.02M   91.8M             0B         0B
FastBoy/ix-apps/app_mounts                                                      108G  33.9G        0B    128K             0B      33.9G
FastBoy/ix-apps/app_mounts/ddns-updater                                         108G  3.16M        0B     96K             0B      3.07M
FastBoy/ix-apps/app_mounts/ddns-updater/data                                    108G  3.07M     2.21M    880K             0B         0B
FastBoy/ix-apps/app_mounts/elastic-search                                       108G   135M        0B     96K             0B       135M
FastBoy/ix-apps/app_mounts/elastic-search/data                                  108G   135M     86.4M   48.7M             0B         0B
FastBoy/ix-apps/app_mounts/gitea                                                108G   504K        0B    120K             0B       384K
FastBoy/ix-apps/app_mounts/gitea/config                                         108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/gitea/data                                           108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/gitea/pgBackup                                       108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/gitea/pgData                                         108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/nextcloud                                            108G   488K        0B    104K             0B       384K
FastBoy/ix-apps/app_mounts/nextcloud/data                                       108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/nextcloud/html                                       108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/nextcloud/pgBackup                                   108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/nextcloud/pgData                                     108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/nginx-proxy-manager                                  108G  37.4M        0B    104K             0B      37.3M
FastBoy/ix-apps/app_mounts/nginx-proxy-manager/certs                            108G  4.84M     3.46M   1.38M             0B         0B
FastBoy/ix-apps/app_mounts/nginx-proxy-manager/data                             108G  32.5M     25.1M   7.37M             0B         0B
FastBoy/ix-apps/app_mounts/ollama                                               108G  32.9G        0B     96K             0B      32.9G
FastBoy/ix-apps/app_mounts/ollama/data                                          108G  32.9G      136K   32.9G             0B         0B
FastBoy/ix-apps/app_mounts/open-webui                                           108G   896M        0B     96K             0B       896M
FastBoy/ix-apps/app_mounts/open-webui/data                                      108G   896M     8.39M    888M             0B         0B
FastBoy/ix-apps/app_mounts/paperless-ngx                                        108G   696K        0B    120K             0B       576K
FastBoy/ix-apps/app_mounts/paperless-ngx/consume                                108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/paperless-ngx/data                                   108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/paperless-ngx/media                                  108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/paperless-ngx/pgBackup                               108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/paperless-ngx/pgData                                 108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/paperless-ngx/trash                                  108G    96K        0B     96K             0B         0B
FastBoy/ix-apps/app_mounts/vaultwarden                                          108G  35.0M        0B    104K             0B      34.9M
FastBoy/ix-apps/app_mounts/vaultwarden/data                                     108G  3.44M     2.82M    636K             0B         0B
FastBoy/ix-apps/app_mounts/vaultwarden/postgres_data                            108G  31.5M     11.4M   20.1M             0B         0B
FastBoy/ix-apps/app_mounts/wg-easy                                              108G  1.33M        0B     96K             0B      1.23M
FastBoy/ix-apps/app_mounts/wg-easy/config                                       108G  1.23M     1.12M    112K             0B         0B
FastBoy/ix-apps/docker                                                          108G   142G      125G   17.1G             0B         0B
FastBoy/ix-apps/truenas_catalog                   

This still shows that the docker folder inside ix-apps is 142G which it should not be. How can I fix this, because as I said it was “removed” when pruning docker. The thing I don’t understand is why is it still here.

You omitted the column headings in your copy-paste. Can you put them on?

root@truenas:/# zfs list -o space
NAME                                                                           AVAIL   USED  USEDSNAP  USEDDS  USEDREFRESERV  USEDCHILD
FastBoy/ix-apps/docker                                                          108G   142G      125G   17.1G             0B         0B

So as you can see in your output you have 125G used by snapshots. The UI is correct. zfsconcepts.7 — OpenZFS documentation

1 Like

Okay I see. I don’t really know why this snapshot does not appear in the GUI under the snapshots page. Can I remove it in some way ? Thanks a lot for your answers

Also, it does not appear when listing snapshots for that path or when sorting all the snapshots by size:

zfs list -r -t snapshot -o name,creation,used -s used 
NAME                                          CREATION                                                                                              USED
[...]

Piscine/Time_Machine/patricia@aapltm-1741446441                                                                              Sat Mar  8 16:07 2025   653M
Piscine/Time_Machine/patricia@aapltm-1742024704                                                                              Sat Mar 15  8:45 2025   655M
Piscine/Time_Machine/patricia@aapltm-1741897649                                                                              Thu Mar 13 21:27 2025   657M
Piscine/Time_Machine/patricia@aapltm-1741442924                                                                              Sat Mar  8 15:08 2025   690M
Piscine/Time_Machine/patricia@aapltm-1741548124                                                                              Sun Mar  9 20:22 2025   699M
Piscine/Time_Machine/patricia@aapltm-1741800178                                                                              Wed Mar 12 18:22 2025   702M
Piscine/Time_Machine/patricia@aapltm-1741435202                                                                              Sat Mar  8 13:00 2025   736M
Piscine/Time_Machine/patricia@aapltm-1741530545                                                                              Sun Mar  9 15:29 2025   753M
Safe/OverleafVM-ytnce9@auto-2025-03-10_00-00                                                                                 Mon Mar 10  0:00 2025  1001M
Piscine/Time_Machine/patricia@auto-2025-03-08_00-00                                                                          Sat Mar  8  0:00 2025  1.10G
Safe/OverleafVM-ytnce9@auto-2025-03-14_00-00                                                                                 Fri Mar 14  0:00 2025  1.12G
Piscine/Time_Machine/patricia@aapltm-1741532525                                                                              Sun Mar  9 16:02 2025  1.12G
Piscine/Time_Machine/patricia@aapltm-1741790333                                                                              Wed Mar 12 15:38 2025  1.31G
Piscine/Time_Machine/patricia@auto-2025-03-04_00-00                                                                          Tue Mar  4  0:00 2025  1.45G
Piscine/Time_Machine/patricia@auto-2025-03-03_00-00                                                                          Mon Mar  3  0:00 2025  1.68G
Safe/OverleafVM-ytnce9@OverleafVM_Backup                                                                                     Sun Feb 23 10:03 2025  2.93G
Piscine/Time_Machine/patricia@auto-2025-03-02_00-00                                                                          Sun Mar  2  0:00 2025  8.06G

You’re looking at wrong property for snapshots. C.f. used, written, written@snapshot zfsprops.7 — OpenZFS documentation

If you have snapshots of the dataset container the data you deleted, then you need to delete all of the snapshots referencing that data before space is actually freed.

Thanks a lot, that was indeed the issue I was confused (and still kinda am) by the used vs referenced parameter. I identified the snapshots and deleted them, the space usage is now shown correct again.

You might find this helpful. It also illustrates why you need to remove all snapshots (“colored sticker sets”) in order to free up more space.