Does LVM eats my disk space or does df lie?

Question

Please look at the output below:

bob ~ # df -h
Filesystem                 Size  Used Avail Use% Mounted on
udev                       5,7G  4,0K  5,7G   1% /dev
tmpfs                      1,2G  1,5M  1,2G   1% /run
/dev/mapper/mint--vg-root  218G   66G  142G  32% /
none                       4,0K     0  4,0K   0% /sys/fs/cgroup
tmpfs                      5,7G  528M  5,2G  10% /tmp
none                       5,0M     0  5,0M   0% /run/lock
none                       5,7G   99M  5,6G   2% /run/shm
none                       100M   48K  100M   1% /run/user
tmpfs                      5,7G   44K  5,7G   1% /var/tmp
/dev/sda1                  236M  132M   93M  59% /boot

df reports that LVM partition has 218G whereas it must be 250G, well 232G if to recalculate with 1024. So where is 14G? But even 218-66=152 not 142! That is 10 more Gigabytes which are also nowhere?

Other utils output:

bob ~ # pvs
  PV         VG      Fmt  Attr PSize   PFree
  /dev/sda5  mint-vg lvm2 a--  232,64g    0 

bob ~ # pvdisplay
  --- Physical volume ---
  PV Name               /dev/sda5
  VG Name               mint-vg
  PV Size               232,65 GiB / not usable 2,00 MiB
  Allocatable           yes (but full)
  PE Size               4,00 MiB
  Total PE              59557
  Free PE               0
  Allocated PE          59557
  PV UUID               3FA5KG-Dtp4-Kfyf-STAZ-K6Qe-ojkB-Tagr83

bob ~ # fdisk -l /dev/sda

Disk /dev/sda: 250.1 GB, 250059350016 bytes
255 heads, 63 sectors/track, 30401 cylinders, total 488397168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x00097b2a

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *        2048      499711      248832   83  Linux
/dev/sda2          501758   488396799   243947521    5  Extended
/dev/sda5          501760   488396799   243947520   8e  Linux LVM

# sfdisk -l -uM

Disk /dev/sda: 30401 cylinders, 255 heads, 63 sectors/track
Warning: extended partition does not start at a cylinder boundary.
DOS and Linux will interpret the contents differently.
Units = mebibytes of 1048576 bytes, blocks of 1024 bytes, counting from 0

   Device Boot Start   End    MiB    #blocks   Id  System
/dev/sda1   *     1    243    243     248832   83  Linux
/dev/sda2       244+ 238474  238231- 243947521    5  Extended
/dev/sda3         0      -      0          0    0  Empty
/dev/sda4         0      -      0          0    0  Empty
/dev/sda5       245  238474  238230  243947520   8e  Linux LVM

Disk /dev/mapper/mint--vg-root: 30369 cylinders, 255 heads, 63 sectors/track

sfdisk: ERROR: sector 0 does not have an msdos signature
 /dev/mapper/mint--vg-root: unrecognized partition table type
No partitions found

Linux Mint 17.3

UPDATE

# lvdisplay
  --- Logical volume ---
  LV Path                /dev/mint-vg/root
  LV Name                root
  VG Name                mint-vg
  LV UUID                ew9fDY-oykM-Nekj-icXn-FQ1T-fiaC-0Jw2v6
  LV Write Access        read/write
  LV Creation host, time mint, 2016-02-18 14:52:15 +0200
  LV Status              available
  # open                 1
  LV Size                232,64 GiB
  Current LE             59557
  Segments               1
  Allocation             inherit
  Read ahead sectors     auto
  - currently set to     256
  Block device           252:0

Regarding swap. Initially it was there, in LVM. Then I removed it and extended root partition with the space which was used by the swap (about 12G)

UPDATE2

# tune2fs -l /dev/mapper/mint--vg-root
tune2fs 1.42.9 (4-Feb-2014)
Filesystem volume name:   <none>
Last mounted on:          /
Filesystem UUID:          0b5ecf9b-a763-4371-b4e7-01c36c47b5cc
Filesystem magic number:  0xEF53
Filesystem revision #:    1 (dynamic)
Filesystem features:      has_journal ext_attr resize_inode dir_index filetype needs_recovery extent flex_bg sparse_super large_file huge_file uninit_bg dir_nlink extra_isize
Filesystem flags:         signed_directory_hash 
Default mount options:    user_xattr acl
Filesystem state:         clean
Errors behavior:          Continue
Filesystem OS type:       Linux
Inode count:              14491648
Block count:              57952256
Reserved block count:     2897612
Free blocks:              40041861
Free inodes:              13997980
First block:              0
Block size:               4096
Fragment size:            4096
Reserved GDT blocks:      1010
Blocks per group:         32768
Fragments per group:      32768
Inodes per group:         8192
Inode blocks per group:   512
Flex block group size:    16
Filesystem created:       Thu Feb 18 14:52:49 2016
Last mount time:          Sun Mar 13 16:49:48 2016
Last write time:          Sun Mar 13 16:49:48 2016
Mount count:              22
Maximum mount count:      -1
Last checked:             Thu Feb 18 14:52:49 2016
Check interval:           0 (<none>)
Lifetime writes:          774 GB
Reserved blocks uid:      0 (user root)
Reserved blocks gid:      0 (group root)
First inode:              11
Inode size:           256
Required extra isize:     28
Desired extra isize:      28
Journal inode:            8
First orphan inode:       6160636
Default directory hash:   half_md4
Directory Hash Seed:      51743315-0555-474b-8a5a-bbf470e3ca9f
Journal backup:           inode blocks

UPDATE3 (Final)

Thanks to Jonas the space loss has been found

# df -h
Filesystem                 Size  Used Avail Use% Mounted on
/dev/mapper/mint--vg-root  218G   65G  142G  32% /


# resize2fs /dev/mapper/mint--vg-root
resize2fs 1.42.9 (4-Feb-2014)
Filesystem at /dev/mapper/mint--vg-root is mounted on /; on-line resizing required
old_desc_blocks = 14, new_desc_blocks = 15
The filesystem on /dev/mapper/mint--vg-root is now 60986368 blocks long.

# df -h
Filesystem                 Size  Used Avail Use% Mounted on
/dev/mapper/mint--vg-root  229G   65G  153G  30% /

and this is a diff of tune2fs command output before and after resize2fs running

# diff /tmp/tune2fs_before_resize2fs /tmp/tune2fs2_after_resize2fs
13,17c13,17
< Inode count:              14491648
< Block count:              57952256
< Reserved block count:     2897612
< Free blocks:              40041861
< Free inodes:              13997980
---
> Inode count:              15253504
> Block count:              60986368
> Reserved block count:     3018400
> Free blocks:              43028171
> Free inodes:              14759836
21c21
< Reserved GDT blocks:      1010
---
> Reserved GDT blocks:      1009
38c38
< Inode size:           256
---
> Inode size:             256
42c42
< First orphan inode:       6160636
---
> First orphan inode:       5904187

Answer 1

Let us do some research. I have noticed that difference before, but never checked in detail what to attribute the losses to. Have a look at my scenario for comparision: fdisk shows the following partition:

/dev/sda3       35657728 1000214527 964556800  460G 83 Linux

There will be some losses as I my filesystem lives in a luks container, but that should only be a few MiB. df shows:

Filesystem      Size  Used Avail Use% Mounted on
/dev/dm-1       453G  373G   58G  87% /

(The luks container is also why /dev/sda3 does not match /dev/dm-1, but they are really the same device, with encryption inbetween, no LVM. This also shows that LVM is not responsible for your losses, I have them too.)

Now lets ask the filesystem itself on that matter. Calling tune2fs -l, which outputs a lot of interesting information about ext-family filesystems, we get:

root@altair ~ › tune2fs -l /dev/dm-1
tune2fs 1.42.12 (29-Aug-2014)
Filesystem volume name:   <none>
Last mounted on:          /
Filesystem UUID:          0de04278-5eb0-44b1-9258-e4d7cd978768
Filesystem magic number:  0xEF53
Filesystem revision #:    1 (dynamic)
Filesystem features:      has_journal ext_attr resize_inode dir_index filetype needs_recovery extent flex_bg sparse_super large_file huge_file uninit_bg dir_nlink extra_isize
Filesystem flags:         signed_directory_hash 
Default mount options:    user_xattr acl
Filesystem state:         clean
Errors behavior:          Continue
Filesystem OS type:       Linux
Inode count:              30146560
Block count:              120569088
Reserved block count:     6028454
Free blocks:              23349192
Free inodes:              28532579
First block:              0
Block size:               4096
Fragment size:            4096
Reserved GDT blocks:      995
Blocks per group:         32768
Fragments per group:      32768
Inodes per group:         8192
Inode blocks per group:   512
Flex block group size:    16
Filesystem created:       Wed Oct 14 09:27:52 2015
Last mount time:          Sun Mar 13 12:25:50 2016
Last write time:          Sun Mar 13 12:25:48 2016
Mount count:              23
Maximum mount count:      -1
Last checked:             Wed Oct 14 09:27:52 2015
Check interval:           0 (<none>)
Lifetime writes:          1426 GB
Reserved blocks uid:      0 (user root)
Reserved blocks gid:      0 (group root)
First inode:              11
Inode size:           256
Required extra isize:     28
Desired extra isize:      28
Journal inode:            8
First orphan inode:       26747912
Default directory hash:   half_md4
Directory Hash Seed:      4723240b-9056-4f5f-8de2-d8536e35d183
Journal backup:           inode blocks

Glancing over it, the first which springs into your eyes should be Reserved blocks. Multiplying that with the Block size (also from the output), we get the difference between the df Used+Avail and Size:

453GiB - (373GiB+58GiB) = 22 GiB
6028454*4096 Bytes = 24692547584 Bytes ~= 23 GiB

Close enough, especially considering that df rounds (using df without -h and repeating the calculation leaves only 16 MiB of the difference between Used+Avail and Size unexplained). To whom the reserved blocks are reserved is also written in the tune2fs output. It is root. This is a safety-net to ensure that non-root users cannot make the system entirely unusable by filling the disk, and keeping a few percent of disk space unused also helps against fragmentation.

Now for the difference between the size reported by df and the size of the partition. This can be explained by taking a look at the inodes. ext4 preallocates inodes, so that space is unusable for file data. Multiply the Inode count by the Inode size, and you get:

30146560*256 Bytes = 7717519360 Bytes ~= 7 GiB
453 GiB + 7 GiB = 460 GiB

Inodes are basically directory entries. Let us ask mkfs.ext4 about details (from man mkfs.ext4):

-i bytes-per-inode

Specify the bytes/inode ratio. mke2fs creates an inode for every bytes-per-inode bytes of space on the disk. The larger the bytes-per-inode ratio, the fewer inodes will be created. This value generally shouldn't be smaller than the blocksize of the filesystem, since in that case more inodes would be made than can ever be used. Be warned that it is not possible to change this ratio on a filesystem after it is created, so be careful deciding the correct value for this parameter. Note that resizing a filesystem changes the numer of inodes to maintain this ratio.

There are different presets to use for different scenarios. On a file server with lots of linux distribution images, it makes sense to pass e.g. -T largefile or even -T largefile4. What -T means is defined in /etc/mke2fs.conf, in those examples and on my system:

largefile = {
    inode_ratio = 1048576
}
largefile4 = {
    inode_ratio = 4194304
}

So with -T largefile4, the number of is much less than the default (the default ratio is 16384 in my /etc/mke2fs.conf). This means, less space reserved for directory entries, and more space for data. When you run out of inodes, you cannot create new files. Increasing the number of inodes in an existing filesystem does not seem to be possible. Thus, the default number of inodes is rather conservatively chosen to ensure that the average user does not run out of inodes prematurely.

I just figured that out at poking at my numbers, let me know if it (does not) work for you ☺.

Answer 2

An easy place to check would be in the logical volume (which does not have to be as large as the physical volume). Use lvdisplay to see the size.

If it does not show a difference there, the usual explanation is that there is space reserved for use by root which does not show in a df by a normal user.

Further reading:

• lvcreate - create a logical volume in an existing volume group
• lvdisplay - display attributes of a logical volume
• Linux LVM Command Example
• Why are partition size and df output different?