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Below is the output when I run ls -l at root home dir:
bin dev home lib64 lost+found mnt proc sbin srv tmp var
boot data.local etc lib license.txt media opt root selinux sys usr
So can I assume /tmp, or /etc, or /lib64 are using the storgae that is 83% full? How to decide which sub directory under / will have its own file system? like, why /var has its own file system? Is it true that one partition will hold one and only one file system?
no, they are not using that, as the clearly have their own partition. This is decided by you or the installer. /var gets filled with logs and such, so you keep it seperate to, amongst other reasons, stop logs making your main disks run out of space. A partition can do loads of things. For example, sda4 on your disk will be an extended partition holding other logical partitions. an LVM partition can also hold an thousand separate filesystems if so desired.