Should /usr and /home be on different partitions?

The 3 primary reasons you would create these as separate partitions are as follows:

1. performance
2. isolation
3. security

Examples

• By separating /home you can put this data on a shared network disk so that when UserA logs into servers in a given domain, their /home/$USER will be a single copy that follows them from machine to machine. This is typically done using NFS and automounts (aka. autofs).

• By putting /usr data on it's own partition, it can be mounted read-only, offering a level of protection to the data under this directory so that it cannot be tampered with so easily.

• Some additional reasoning for isolating /usr, is for making it easier to deploy identical systems, these partitions can be prepared one time and then replicated across systems more easily.

• Also separating the data out can make it easier for backup cycles.

• Finally separating volatile directories such as /home can protect a system from having it's primary disk fill up by either an accidental or malicious user.

Over the course of my 15+ years of doing this I've only ever seen /home separated (as a network share via NFS) and the /boot and /var directories as being isolated as separate partitions. Outside of some esoteric Solaris boxes I can't recall ever seeing a Linux system having a separate /usr - and note that if you don't have /usr mounted before init starts, your system will break in esoteric and silent ways.

Putting /home on a separate partition is fairly common. That typically splits system files (/) and user files (/home). The two filesystems may have different performance trade-offs, different backup policies, different quotas, different security policies, etc. Also this way the OS can be reinstalled or reimaged independently of the user data. Splitting /home is a good idea both for single-user workstations and for multi-user systems that store user files. I'd only keep /home on the same partition on a server that has no user files beyond the administrators' configuration files (but there might be a separate partition for whatever that machine is about — /var/mail, or a database, etc.), or on a quick-and-simple installation especially on a laptop which isn't going to be rebalanced to use a second disk.

Putting /usr on a separate partition used to be common, back when the OS used a large amount of disk space (say, 300MB out of 1GB). This partition could be made read-only, might be shared over the network. Making /usr read-only had the advantage that in case of a power loss, it wouldn't need an fsck. Nowadays all major filesystems use a journal and don't require any lengthy fsck, and disk sizes have increased a lot more than OS sizes — 30GB out of 1TB is peanuts, so it doesn't need to be shared. There is no good reason to split /usr from the rest of the system (/bin, /etc, /var, …). If you see advice to split /usr, it's grossly obsolete.

It is common to separate /usr and /home. There are a number of reasons for this. Here are a few:

Encryption

Although encrypting the contents of /usr can have some benefits, it is common to dedicate full encrypted partitions to /home directories and leave /usr unencrypted.

Different drives

I am currently using a laptop that has a small SSD and a large hard drive. The root partition, which includes /usr, is on the SSD. /home is on the hard drive. SSDs wear down relatively quickly as they are written to. Putting volatile directories such as /home and /var on the SSD would decrease its lifespan significantly. Putting my root partition on the SSD decreases my machine's boot time.

Security

It is common to mount /home directories with the nosetuid option. This option disallows the execution of setuid files on a mount. Setting this option makes it more difficult for users to hide away root-owned setuid shells.