Files on disk have two sizes: the "apparent size" and the "size on disk". Several reasons can cause a large discrepancy:

• A large number of files will result in a large amount of overhead, because of internal fragmentation. E.g. Ext4 has a 4KiB default block size; files smaller than that will consume always 4KiB, and sizes above will be "rounded" to this block alignment.


• Directories are also files and the same rule applies for them as well. Moreover, if you would create a large amount of files in a directory, and remove them again later, the usage on the directory file can't be reclaimed (recreating the directory helps).


• Sparse files are special files, that appear to be large, but aren't 'consuming' the space. This is common in virtualization for virtual disk images; they will appear large, but the 'real' size can be a lot smaller. A lot of utilities (and file managers) are incapable of showing the actual disk usage.


• The use of hard links. The contents of a file can exist on disk while multiple references are pointing to it. Some file managers may account the size for every reference.

I would suggest to use a disk usage tool known to be capable of listing both sizes to see if this is the issue. Try ncdu in a terminal and use a to toggle between actual and disk usage.

A short demo on internal fragmentation due to a 4KiB block size filesystem using du:

$ sudo tune2fs -l /dev/path-to-device | grep "Block size"

Block size:               4096



$ echo blaataaap > myfile                      # creates a 10-byte file



$ du --block-size=1 myfile                     # prints the usage on disk (filesystem)

4096   myfile



$ du --apparent-size --block-size=1 myfile     # prints the apparent size, i.e.

10     myfile                                  # content length when seeking



$ ls -al

-rw-rw-r-- 1 gert gert 10 Jan 1 23:24 myfile   # ls uses apparent sizes

This means that this 10-byte file is 4086 bytes bigger on disk than it would appear in a listing and is suffering from internal fragmentation.

A short demo on hard links and disk usage shown wrong when listing files (ls in this case):

$ dd if=/dev/zero of=1MBfile bs=1M count=1 # create a 1MB file

$ ln 1MBfile a_hard_link                   # create a hard link to it



$ ls -alht                                 # ls will report 2MB

total 2.1M

drwxrwxr-x  2 gert gert 4.0K Jan  2 11:21 .

-rw-rw-r--  2 gert gert 1.0M Jan  2 11:21 1MBfile

-rw-rw-r--  2 gert gert 1.0M Jan  2 11:21 a_hard_link



$ du -B 1024 .                             # du reports 1028K total for directory

1028    .



$ du -B 1024 a_hard_link                   # and 1024K for each file individually

1024    a_hard_link

$ du -B 1024 1MBfile

1024    1MBfile