No more space on FreeNAS 9.3. But only half of space actually in use based on "du -sh" command

8,778

I try to sum up the given information and give some explanation (where I know, what it means):

About the zpool list output:
SIZE is the size of all discs, including the discs used for redundancy (so together with the output of zpool status that means, you have put together 8 3TB drives in a RAID-Z3 configuration)
ALLOC is the used space, also including the discs used for redundancy (so it is at least (5+3)/5=1,6 times higher than the real data size, because 3 of the 8 discs are used for redundancy)
Free is the free space, also including the discs used for redundancy (so the usable free space is at most 5/(5+3)=0,625 the shown free size)

The zfs list command says, there is 1,34T available, zpool list says 3,16T free, minus the redundancy space I would expect about 1,975T.
I know, that zfs needs some space for metadata, but on my linux system with 4 2TB drives in RAID-Z1 the difference is about 6%, your difference here is about 47%, I can't say where the difference come from.

About the output of df -Th
df doesn't find zfs snapshots, so it can't calculate them, so the space used is not the space used in the zfs filesystem. For allocated space in the zfs filesystem, use zfs list

Deleting snapshots can take time as you found out, seems to be by design, you can take a look at http://nex7.blogspot.de/2013/03/readme1st.html

After deleting the snapshots, if I count your df output, you have about 7,2T of data in your pool and about 4T free, making 11,2T all.
If I take your complete size (21,8T) minus the redundancy discs, I would expect about 5/(5+3)*21,8T=13,6T (a difference about 20%)

I think 20% is a little bit to much for the metadata needed by zfs, but I can't tell you, where it get lost. Maybe you have many very small files, which are using more metadata space than not so many bigger files.
I'm sorry, but I'm not so deep in the zfs internals, that I can tell you, where to get the metadata space usage.
You could try again a zfs list and compare the used space there with the used space you get from df. Maybe it gives a hint.

Edited 21.07.2015
About the size: 3T drives have actually 2,7 TiB (because the drive manufactures are using 1TB = 1.000.000.000.000 Bytes, where Computers using 1TiB = 1*1024*1024*1024*1024=1.099.511.627.776 Bytes.
2,7 * 8 drives = 21,8T
In normal RAID Systems, the smallest drive determines the usable size of the larger drives.

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陳敬翔
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陳敬翔

Updated on September 18, 2022

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  • 陳敬翔
    陳敬翔 almost 2 years

    This morning I got a warning on my FreeNAS 9.3 machine about "Not enough space"

    warning: The capacity for the volume 'SeanVolume' is currently at 85%, while the recommended value is below 80%.
    

    It's of no use running the scrub command after a period of time.

    I used SSH to login to FreeNAS host, and got some information:

    [root@freenas] ~# zpool list
    NAME           SIZE  ALLOC   FREE  EXPANDSZ   FRAG    CAP  DEDUP  HEALTH  ALTROOT
    SeanVolume    21.8T  18.6T  3.16T         -    38%    85%  1.00x  ONLINE  /mnt
    freenas-boot   111G   680M   110G         -      -     0%  1.00x  ONLINE  -
    

    It shows it's ALLOC space only at 18.6T capacity, but it still had 6.7T by du -sh command:

    [root@freenas] ~# du -sh /mnt/SeanVolume/
    6.7T    /mnt/SeanVolume/
    

    Additional information:

    [root@freenas] ~# zpool status
      pool: SeanVolume
     state: ONLINE
      scan: scrub repaired 0 in 20h32m with 0 errors on Thu Jul 16 07:48:34 2015
    config:
    
            NAME                                            STATE     READ WRITE CKSUM
            SeanVolume                                      ONLINE       0     0     0
              raidz3-0                                      ONLINE       0     0     0
                gptid/f4986ea8-f822-11e4-a7d4-d05099265144  ONLINE       0     0     0
                gptid/f51a05f7-f822-11e4-a7d4-d05099265144  ONLINE       0     0     0
                gptid/f595d78e-f822-11e4-a7d4-d05099265144  ONLINE       0     0     0
                gptid/f62490d4-f822-11e4-a7d4-d05099265144  ONLINE       0     0     0
                gptid/f6a8e41e-f822-11e4-a7d4-d05099265144  ONLINE       0     0     0
                gptid/f7266471-f822-11e4-a7d4-d05099265144  ONLINE       0     0     0
                gptid/f7f3bf28-f822-11e4-a7d4-d05099265144  ONLINE       0     0     0
                gptid/f8b8fa7b-f822-11e4-a7d4-d05099265144  ONLINE       0     0     0
            cache
              gptid/f901ec00-f822-11e4-a7d4-d05099265144    ONLINE       0     0     0
              gptid/dfa53351-1baa-11e5-ba0e-d05099265144    ONLINE       0     0     0
    
    errors: No known data errors
    

    Result of df -TH command:

    [root@freenas] ~# df -TH
    Filesystem                                                  Type      Size    Used   Avail Capacity  Mounted on
    freenas-boot/ROOT/default                                   zfs       115G    698M    114G     1%    /
    devfs                                                       devfs     1.0k    1.0k      0B   100%    /dev
    tmpfs                                                       tmpfs      33M    5.5M     28M    16%    /etc
    tmpfs                                                       tmpfs     4.2M    8.2k    4.2M     0%    /mnt
    tmpfs                                                       tmpfs      11G     67M     11G     1%    /var
    freenas-boot/grub                                           zfs       114G    8.1M    114G     0%    /boot/grub
    SeanVolume                                                  zfs       1.6T    822k    1.6T     0%    /mnt/SeanVolume
    SeanVolume/CandyDataset                                     zfs       1.6T    299k    1.6T     0%    /mnt/SeanVolume/CandyDataset
    SeanVolume/CandyDataset/Applications                        zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/CandyDataset/Applications
    SeanVolume/CandyDataset/Documents                           zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/CandyDataset/Documents
    SeanVolume/CandyDataset/Downloads                           zfs       2.9T    1.3T    1.6T    46%    /mnt/SeanVolume/CandyDataset/Downloads
    SeanVolume/CandyDataset/Music                               zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/CandyDataset/Music
    SeanVolume/CandyDataset/Pictures                            zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/CandyDataset/Pictures
    SeanVolume/CandyDataset/Temporary                           zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/CandyDataset/Temporary
    SeanVolume/CandyDataset/Videos                              zfs       1.8T    221G    1.6T    12%    /mnt/SeanVolume/CandyDataset/Videos
    SeanVolume/PublicDataset                                    zfs       1.6T    243k    1.6T     0%    /mnt/SeanVolume/PublicDataset
    SeanVolume/PublicDataset/Applications                       zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/PublicDataset/Applications
    SeanVolume/PublicDataset/Documents                          zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/PublicDataset/Documents
    SeanVolume/PublicDataset/Downloads                          zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/PublicDataset/Downloads
    SeanVolume/PublicDataset/Music                              zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/PublicDataset/Music
    SeanVolume/PublicDataset/Pictures                           zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/PublicDataset/Pictures
    SeanVolume/PublicDataset/Temporary                          zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/PublicDataset/Temporary
    SeanVolume/PublicDataset/Videos                             zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/PublicDataset/Videos
    SeanVolume/SeanDataset                                      zfs       3.9T    2.3T    1.6T    60%    /mnt/SeanVolume/SeanDataset
    SeanVolume/SeanDataset/AppData                              zfs       1.6T    224k    1.6T     0%    /mnt/SeanVolume/SeanDataset/AppData
    SeanVolume/SeanDataset/Applications                         zfs       1.6T    261k    1.6T     0%    /mnt/SeanVolume/SeanDataset/Applications
    SeanVolume/SeanDataset/Documents                            zfs       3.0T    1.5T    1.6T    48%    /mnt/SeanVolume/SeanDataset/Documents
    SeanVolume/SeanDataset/Downloads                            zfs       2.2T    647G    1.6T    29%    /mnt/SeanVolume/SeanDataset/Downloads
    SeanVolume/SeanDataset/Music                                zfs       1.6T    411k    1.6T     0%    /mnt/SeanVolume/SeanDataset/Music
    SeanVolume/SeanDataset/Pictures                             zfs       1.6T    2.2M    1.6T     0%    /mnt/SeanVolume/SeanDataset/Pictures
    SeanVolume/SeanDataset/Saved Games                          zfs       1.6T    243k    1.6T     0%    /mnt/SeanVolume/SeanDataset/Saved Games
    SeanVolume/SeanDataset/Temporary                            zfs       1.6T    533k    1.6T     0%    /mnt/SeanVolume/SeanDataset/Temporary
    SeanVolume/SeanDataset/Videos                               zfs       2.4T    850G    1.6T    35%    /mnt/SeanVolume/SeanDataset/Videos
    SeanVolume/jails                                            zfs       1.6T    710M    1.6T     0%    /mnt/SeanVolume/jails
    SeanVolume/jails/.warden-template-pluginjail                zfs       1.6T    619M    1.6T     0%    /mnt/SeanVolume/jails/.warden-template-pluginjail
    SeanVolume/jails/.warden-template-pluginjail-9.3            zfs       1.6T    619M    1.6T     0%    /mnt/SeanVolume/jails/.warden-template-pluginjail-9.3
    SeanVolume/jails/pluginjail                                 zfs       1.6T    660M    1.6T     0%    /mnt/SeanVolume/jails/pluginjail
    SeanVolume/ownCloudDataset                                  zfs       1.8T    259G    1.6T    14%    /mnt/SeanVolume/ownCloudDataset
    SeanVolume/.system                                          zfs       1.6T    3.4M    1.6T     0%    /var/db/system
    SeanVolume/.system/cores                                    zfs       1.6T    1.4M    1.6T     0%    /var/db/system/cores
    SeanVolume/.system/samba4                                   zfs       1.6T      6M    1.6T     0%    /var/db/system/samba4
    SeanVolume/.system/syslog-cd1fc29ce94d4a81a24df77359252261  zfs       1.6T      6M    1.6T     0%    /var/db/system/syslog-cd1fc29ce94d4a81a24df77359252261
    SeanVolume/.system/rrd-cd1fc29ce94d4a81a24df77359252261     zfs       1.6T    224k    1.6T     0%    /var/db/system/rrd-cd1fc29ce94d4a81a24df77359252261
    devfs                                                       devfs     1.0k    1.0k      0B   100%    /mnt/SeanVolume/jails/pluginjail/dev
    procfs                                                      procfs    4.1k    4.1k      0B   100%    /mnt/SeanVolume/jails/pluginjail/proc
    SeanVolume/jails/customplugin_2                             zfs       1.6T    1.4G    1.6T     0%    /mnt/SeanVolume/jails/customplugin_2
    SeanVolume/SeanDataset/ISOImage                             zfs       1.6T    318k    1.6T     0%    /mnt/SeanVolume/SeanDataset/ISOImage
    devfs                                                       devfs     1.0k    1.0k      0B   100%    /mnt/SeanVolume/jails/customplugin_2/dev
    procfs                                                      procfs    4.1k    4.1k      0B   100%    /mnt/SeanVolume/jails/customplugin_2/proc
    /mnt/SeanVolume/ownCloudDataset                             nullfs    1.8T    259G    1.6T    14%    /mnt/SeanVolume/jails/customplugin_2/media
    

    Running the scrub status (Web GUI):

    Scrub status: Completed
    Errors: 0     Repaired: 0     Date: Thu Jul 16 07:48:34 2015
    

    What can I do to attempt to fix this (except reboot, because it is running ownCloud Plugin online)?


    PS: 2015/07/17 Added:

    [root@freenas] ~# zfs list
    NAME                                                         USED  AVAIL  REFER  MOUNTPOINT
    SeanVolume                                                  10.7T  1.34T   803K  /mnt/SeanVolume
    SeanVolume/.system                                           304M  1.34T  3.21M  legacy
    SeanVolume/.system/cores                                    5.53M  1.34T  1.32M  legacy
    SeanVolume/.system/rrd-cd1fc29ce94d4a81a24df77359252261      219K  1.34T   219K  legacy
    SeanVolume/.system/samba4                                    218M  1.34T  5.59M  legacy
    SeanVolume/.system/syslog-cd1fc29ce94d4a81a24df77359252261  61.4M  1.34T  5.62M  legacy
    SeanVolume/CandyDataset                                     1.42T  1.34T   292K  /mnt/SeanVolume/CandyDataset
    SeanVolume/CandyDataset/Applications                         365K  1.34T   219K  /mnt/SeanVolume/CandyDataset/Applications
    SeanVolume/CandyDataset/Documents                            365K  1.34T   219K  /mnt/SeanVolume/CandyDataset/Documents
    SeanVolume/CandyDataset/Downloads                           1.22T  1.34T  1.22T  /mnt/SeanVolume/CandyDataset/Downloads
    SeanVolume/CandyDataset/Music                                365K  1.34T   219K  /mnt/SeanVolume/CandyDataset/Music
    SeanVolume/CandyDataset/Pictures                             365K  1.34T   219K  /mnt/SeanVolume/CandyDataset/Pictures
    SeanVolume/CandyDataset/Temporary                            365K  1.34T   219K  /mnt/SeanVolume/CandyDataset/Temporary
    SeanVolume/CandyDataset/Videos                               206G  1.34T   206G  /mnt/SeanVolume/CandyDataset/Videos
    SeanVolume/PublicDataset                                    3.03M  1.34T   237K  /mnt/SeanVolume/PublicDataset
    SeanVolume/PublicDataset/Applications                        365K  1.34T   219K  /mnt/SeanVolume/PublicDataset/Applications
    SeanVolume/PublicDataset/Documents                           365K  1.34T   219K  /mnt/SeanVolume/PublicDataset/Documents
    SeanVolume/PublicDataset/Downloads                           365K  1.34T   219K  /mnt/SeanVolume/PublicDataset/Downloads
    SeanVolume/PublicDataset/Music                               365K  1.34T   219K  /mnt/SeanVolume/PublicDataset/Music
    SeanVolume/PublicDataset/Pictures                            365K  1.34T   219K  /mnt/SeanVolume/PublicDataset/Pictures
    SeanVolume/PublicDataset/Temporary                           365K  1.34T   219K  /mnt/SeanVolume/PublicDataset/Temporary
    SeanVolume/PublicDataset/Videos                              365K  1.34T   219K  /mnt/SeanVolume/PublicDataset/Videos
    SeanVolume/SeanDataset                                      8.04T  1.34T  2.14T  /mnt/SeanVolume/SeanDataset
    SeanVolume/SeanDataset/AppData                              2.64M  1.34T   219K  /mnt/SeanVolume/SeanDataset/AppData
    SeanVolume/SeanDataset/Applications                          178G  1.34T   256K  /mnt/SeanVolume/SeanDataset/Applications
    SeanVolume/SeanDataset/Documents                            2.58T  1.34T  1.33T  /mnt/SeanVolume/SeanDataset/Documents
    SeanVolume/SeanDataset/Downloads                            1.07T  1.34T   661G  /mnt/SeanVolume/SeanDataset/Downloads
    SeanVolume/SeanDataset/ISOImage                              103G  1.34T   310K  /mnt/SeanVolume/SeanDataset/ISOImage
    SeanVolume/SeanDataset/Music                                51.7G  1.34T   402K  /mnt/SeanVolume/SeanDataset/Music
    SeanVolume/SeanDataset/Pictures                              131G  1.34T  2.08M  /mnt/SeanVolume/SeanDataset/Pictures
    SeanVolume/SeanDataset/Saved Games                          75.7G  1.34T   237K  /mnt/SeanVolume/SeanDataset/Saved Games
    SeanVolume/SeanDataset/Temporary                            9.63G  1.34T   520K  /mnt/SeanVolume/SeanDataset/Temporary
    SeanVolume/SeanDataset/Videos                                846G  1.34T   792G  /mnt/SeanVolume/SeanDataset/Videos
    SeanVolume/jails                                            3.80G  1.34T   678M  /mnt/SeanVolume/jails
    SeanVolume/jails/.warden-template-pluginjail                6.33M  1.34T   591M  /mnt/SeanVolume/jails/.warden-template-pluginjail
    SeanVolume/jails/.warden-template-pluginjail-9.3             597M  1.34T   591M  /mnt/SeanVolume/jails/.warden-template-pluginjail-9.3
    SeanVolume/jails/customplugin_2                             1.17G  1.34T  1.27G  /mnt/SeanVolume/jails/customplugin_2
    SeanVolume/jails/pluginjail                                 1.28G  1.34T   630M  /mnt/SeanVolume/jails/pluginjail
    SeanVolume/ownCloudDataset                                  1.21T  1.34T   255G  /mnt/SeanVolume/ownCloudDataset
    freenas-boot                                                 680M   107G   144K  none
    freenas-boot/ROOT                                            670M   107G   144K  none
    freenas-boot/ROOT/Initial-Install                              8K   107G   659M  legacy
    freenas-boot/ROOT/default                                    670M   107G   665M  legacy
    freenas-boot/grub                                           7.76M   107G  7.76M  legacy
    

    2015/07/17 Added:

    After I used zfs list -t snapshot command, it show off many tiny snapshots (totally 2,534 files...).

    I am checking, and delete those snapshot files.

    After delete, running df -TH again!


    2015/07/20 Add:

    I got some space after I delete many snapshot files!

    but...

    The FreeNAS 9.3 Web GUI crashed...

    After I clear a large number of Snapshots (approximately 1500), FreeNAS 9.3 Web GUI displays "An error occurred." After two days

    [root@freenas] /etc/defaults# df -TH
    Filesystem                                                  Type      Size    Used   Avail Capacity  Mounted on
    freenas-boot/ROOT/default                                   zfs       115G    698M    114G     1%    /
    devfs                                                       devfs     1.0k    1.0k      0B   100%    /dev
    tmpfs                                                       tmpfs      33M    5.5M     28M    16%    /etc
    tmpfs                                                       tmpfs     4.2M    8.2k    4.2M     0%    /mnt
    tmpfs                                                       tmpfs      11G     67M     11G     1%    /var
    freenas-boot/grub                                           zfs       114G    8.1M    114G     0%    /boot/grub
    SeanVolume                                                  zfs         4T    822k      4T     0%    /mnt/SeanVolume
    SeanVolume/CandyDataset                                     zfs         4T    299k      4T     0%    /mnt/SeanVolume/CandyDataset
    SeanVolume/CandyDataset/Downloads                           zfs       5.3T    1.3T      4T    25%    /mnt/SeanVolume/CandyDataset/Downloads
    SeanVolume/CandyDataset/Videos                              zfs       4.2T    221G      4T     5%    /mnt/SeanVolume/CandyDataset/Videos
    SeanVolume/PublicDataset                                    zfs         4T    224k      4T     0%    /mnt/SeanVolume/PublicDataset
    SeanVolume/SeanDataset                                      zfs       9.6T    5.6T      4T    59%    /mnt/SeanVolume/SeanDataset
    SeanVolume/jails                                            zfs         4T    710M      4T     0%    /mnt/SeanVolume/jails
    SeanVolume/jails/.warden-template-pluginjail                zfs         4T    619M      4T     0%    /mnt/SeanVolume/jails/.warden-template-pluginjail
    SeanVolume/jails/.warden-template-pluginjail-9.3            zfs         4T    619M      4T     0%    /mnt/SeanVolume/jails/.warden-template-pluginjail-9.3
    SeanVolume/jails/pluginjail                                 zfs         4T    661M      4T     0%    /mnt/SeanVolume/jails/pluginjail
    SeanVolume/ownCloudDataset                                  zfs       4.3T    336G      4T     8%    /mnt/SeanVolume/ownCloudDataset
    SeanVolume/.system                                          zfs         4T    3.4M      4T     0%    /var/db/system
    SeanVolume/.system/cores                                    zfs         4T    1.4M      4T     0%    /var/db/system/cores
    SeanVolume/.system/samba4                                   zfs         4T    6.1M      4T     0%    /var/db/system/samba4
    SeanVolume/.system/syslog-cd1fc29ce94d4a81a24df77359252261  zfs         4T     11M      4T     0%    /var/db/system/syslog-cd1fc29ce94d4a81a24df77359252261
    SeanVolume/.system/rrd-cd1fc29ce94d4a81a24df77359252261     zfs         4T    224k      4T     0%    /var/db/system/rrd-cd1fc29ce94d4a81a24df77359252261
    devfs                                                       devfs     1.0k    1.0k      0B   100%    /mnt/SeanVolume/jails/pluginjail/dev
    procfs                                                      procfs    4.1k    4.1k      0B   100%    /mnt/SeanVolume/jails/pluginjail/proc
    SeanVolume/jails/customplugin_2                             zfs         4T    1.4G      4T     0%    /mnt/SeanVolume/jails/customplugin_2
    devfs                                                       devfs     1.0k    1.0k      0B   100%    /mnt/SeanVolume/jails/customplugin_2/dev
    procfs                                                      procfs    4.1k    4.1k      0B   100%    /mnt/SeanVolume/jails/customplugin_2/proc
    /mnt/SeanVolume/ownCloudDataset                             nullfs    4.3T    336G      4T     8%    /mnt/SeanVolume/jails/customplugin_2/media
    
    • Admin
      Admin almost 9 years
      zpool list includes in ALLOC the space needed for the parity Information. So ALLOC in zpool list is always more than a du shows. Try zfs list and post the output.
    • Admin
      Admin almost 9 years
      Could it be, that you use zfs snapshots? They will also allocate space, but will probably not be visible in a simple du command. You can find snapshots and the space they will use with a zfs list -t snapshot command.
  • 陳敬翔
    陳敬翔 almost 9 years
    I really appreciate your detail-minded explanations, I learned a lot! In fact, I'm not sure why: I actually used the 6 3TB and 2 4T, which theoretically should have 24 ~ 26T, but last only 21.8 TB. Finally it's only 12.1TB after redundancy. And why a difference of 20%, it's possible to wait other ZFS experts to answer. Thank you very much!
  • aaaaa says reinstate Monica
    aaaaa says reinstate Monica almost 9 years
    I have 24x1TB array in 4xRAIDZ2 (2 disk of redundancy per every 6 disks, theoretical volume of 16TB) and zpool list shows 21.8TB. zfs list shows 13.3T. It seems that zpool list shows space projected for compression.
  • Sunzi
    Sunzi almost 9 years
    No. zpool list shows space including the redundancy drives. 1TB=0,909 TiB. 0,909Tib*24=21,8TiB so zpool list shows simply the complet space all drives have. zfs list shows the usable space (minus redundancy, minus metadata)