Most secure way to partition linux?

Please keep in mind the Holy Trinity of Information Security: C(onfidentiality), I(ntegrity), and A(vailability). So when we talk about configuration hardening you need to consider the technology you're working with, the information being protected, how the information is used within the organization, and the threats. Based on those answers, and possibly others, you can begin to determine which of the tenants are most important and what to focus on.

At the filesystem level you're typically most interested in Integrity and Availability. The Confidentiality of the information should probably be handled at a different layer, but how you lay our your filesystems and how you use them should make sure that the information is both trustworthy and is always available when it's needed.

One thing to keep in mind when laying out your partitions are failure modes. Typically that question is of the form: "What happens when partition x fills up?"

What happens if your partition storing the OS is full? Strange things sometimes happen when / fills up. Sometimes the system hangs. Sometimes no new login sessions can occur. Sometimes the system refuses to boot.

Of all the failure modes this one is the hardest to strictly characterize as its symptoms are the most likely to change based on OS, kernel version, configuration, etc. Some filesystems, particularly the ext line, reserve a certain amount of space when the filesystem is created. This reseved space can only be used by the root user and is intended to allow the systems administrator to still operate and clean out space.

What happens if your partition storing logs is full? You lose auditing/reporting data and is sometimes used by attackers to hide their activity. In some cases your system will not authenticate new users if it can't record their login event.

What happens on an RPM based system when /var is full? The package manager will not install or update packages and, depending on your configuration, may fail silently.

Filling up a partition is easy, especially when a user is capable of writing to it. For fun, run this command and see how quickly you can make a pretty big file: cat /dev/zero > zerofile.

It goes beyond filling up partitions as well, when you place locations on different mount points you can also customize their mount options.

What happens when /dev/ is not mounted with noexec? Since /dev is typically assumed to be maintained by the OS and only contain devices it was frequently (and sometimes still is) used to hide malicious programs. Leaving off noexec allows you do launch binaries stored there.

For all these reasons, and more, many hardening guides will discuss partitioning as one of the first steps to be performed. In fact, if you are building a new server how to partition the disk is very nearly exactly the first thing you have to decide on, and often the most difficult to later change. There exists a group called the Center for Internet Security that produces gobs of easy to read configuration guides. You can likely find a guide for your specific Operating System and see any specifics they may say.

If we look at RedHat Enterprise Linux 6, the recommended partitioning scheme is this:

# Mount point           Mount options
/tmp                    nodev,nosuid,noexec
/var                    
/var/tmp                bind (/tmp)
/var/log
/var/log/audit
/home                   nodev
/dev/shm                nodev,nosuid,noexec

The principle behind all of these changes are to prevent them from impacting each other and/or to limit what can be done on a specific partition. Take the options for /tmp for example. What that says is that no device nodes can be created there, no programs can be executed from there, and the set-uid bit can't be set on anything. By its very nature, /tmp is almost always world writable and is often a special type of filesystem that only exists in memory. This means that an attacker could use it as an easy staging point to drop and execute malicious code, then crashing (or simply rebooting) the system will wipe clean all the evidence. Since the functionality of /tmp doesn't require any of that functionality, we can easily disable the features and prevent that situation.

The log storage places, /var/log and /var/log/audit are carved off to help buffer them from resource exhaustion. Additionally, auditd can perform some special things (typically in higher security environments) when its log storage begins to fill up. By placing it on its partition this resource detection performs better.

To be more verbose, and quote mount(8), this is exactly what the above used options are:

noexec Do not allow direct execution of any binaries on the mounted file system. (Until recently it was possible to run binaries anyway using a command like /lib/ld*.so /mnt/binary. This trick fails since Linux 2.4.25 / 2.6.0.)

nodev Do not interpret character or block special devices on the file system.

nosuid Do not allow set-user-identifier or set-group-identifier bits to take effect. (This seems safe, but is in fact rather unsafe if you have suidperl(1) installed.)

From a security perspective these are very good options to know since they'll allow you to put protections on the filesystem itself. In a highly secure environment you may even add the noexec option to /home. It'll make it harder for your standard user to write shell scripts for processing data, say analyzing log files, but it will also prevent them from executing a binary that will elevate privileges.

Also, keep in mind that the root user's default home directory is /root. This means it will be in the / filesystem, not in /home.

Exactly how much you give to each partition can vary greatly depending on the systems workload. A typical server that I've managed will rarely require person interaction and as such the /home partition doesn't need to be very big at all. The same applies to /var since it tends to store rather ephemeral data that gets created and deleted frequently. However, a web server typically uses /var/www as its playground, meaning that either that needs to be on a separate partition as well or /var/ needs to be made big.

In the past I have recommended the following as baselines.

# Mount Point       Min Size (MB)    Max Size (MB)
/                   4000             8000
/home               1000             4000
/tmp                1000             2000
/var                2000             4000
swap                1000             2000
/var/log/audit       250

These need to be reviewed and adjusted according to the system's purpose, and how your environment operates. I would also recommend using LVM and against allocating the entire disk. This will allow you to easily grow, or add, partitions if such things are required.

The split into one or several partitions is not really a problem of security but of reliability. The idea is that if one of your partitions is crashed, then you lose the contents of that partition, but the other partitions are fine. Also, if you fill up that partition, then other partitions are unaffected. Each partition can have its own filesystem, and not all types of filesystems are equivalent with regards to performance in various contexts (although most filesystems will be mostly as good as each other in most contexts). On some PC, the boot process may have trouble access farther than the first few gigabytes of the disk due to historical peculiarities of this architecture, which are too horrifying to be recalled here; thus, /boot is often better set as a separate partition of limited size and located first in the disk.

If you want to apply partition-level encryption, then you may run into trouble if you encrypt too much -- namely, the code which does the decryption must be located outside of the said partition. This depends a lot on the actual encryption product (some can embed the decryption code in the bootloader).

Note that the more you split your disk into partitions, the less flexible the whole thing becomes. When a partition fills up, it is full and stays that way, even if other partitions have free space (LVM can help cope with that, so you might want to say "yes" when the OS installer asks whether you want to use LVM). The more partitions you create, the more probable and hard this problem becomes.

The easy and safe path is to let the OS installer choose the partitions as it thinks best. Don't go on changing partition sizes until you have some precise knowledge and experience of what this entails. Don't forget to make regular backups. It is expected that, after a few months, you will want to reinstall your OS to "do it right", and that's not necessarily a bad idea, so don't sweat it. This is a learning tool, not a server which will go into production.

I'd look at this a different way than the other responders so far: if you are looking at a bunch of exploits, then all the threats are possible and sandboxing the system where you do that as much as possible seems like a useful precaution. Xen is one easy way to do that. It can use disk images on another file system, but if you know you are going to use it I'd suggest leaving separate disk partitions (and make sure they don't get automounted on your Dom0).

I don't know how well Kali works as Xen Dom0. Ubuntu at least seems to have issues. You might consider leaving room for XenServer or another specialized Xen Dom0 build. [Edit: I'm not sure what netbooks are like these days but I'm guessing XenServer isn't really targeting them... Maybe some other simpler distribution that works well with Xen as Dom0. You may be able to set up a Kali install that runs either standalone or as a DomU if looking at exploits is a less common task.]

On BSD systems I've heard of hardening methods involving partitioning to mount as much as possible read only and using immutable flags. I'd assume there are at least some Linux systems where a similar setup is possible, however it looks like Kali is Debian based and my sense is that you can't really do that on Debian [edit: unless you mount a writeable FS over it, which would still be awkward to maintain over time]. In any case, I wouldn't suggest this for a general purpose machine and only bring it up in case you are more generally interested in all the ways partitioning might be used. For your purpose, put the threats on a system you can delete and recreate easily.