FWIW, Debian 9 (stretch) has it set to "madvise", but my Debian unstable machine has it to "always". Looking further, I can see that /boot/config-4.12.0-1-amd64 has:

  # CONFIG_TRANSPARENT_HUGEPAGE_ALWAYS is not set
  CONFIG_TRANSPARENT_HUGEPAGE_MADVISE=y

and /boot/config-4.13.0-1-amd64 has:

  CONFIG_TRANSPARENT_HUGEPAGE_ALWAYS=y
  # CONFIG_TRANSPARENT_HUGEPAGE_MADVISE is not set

So this is a recent change.

Edit: The linux kernel source says the default is always (in mm/Kconfig), and that's been true since 2011.

The debian package changelog says the change occurred in 4.13.4-1:

  * thp: Enable TRANSPARENT_HUGEPAGE_ALWAYS instead of
    TRANSPARENT_HUGEPAGE_MADVISE

The reason is not given in the changelog itself, but it's given in the git log of the debian packaging:

As advised by Andrea Arcangeli - since commit 444eb2a449ef "mm: thp: set THP defrag by default to madvise and add a stall-free defrag option" this will generally be best for performance.

https://anonscm.debian.org/cgit/kernel/linux.git/commit/debi...

Edit 2: The mentioned commit (444eb2a449ef) dates back to 4.6, so presumably, at least some performance issues with transparent huge pages may be gone since that version of the kernel.

Interesting. I'm running Debian unstable, and recently my system would sometimes lock up under heavy memory pressure. I'm using VirtualBox, which has its own kernel module, so I can't be sure Linux itself is to blame, but the timing seems to coincide with when I switched to that kernel version. Maybe transparent hugepages uncovered a VirtualBox bug or even a kernel bug. And I care about worst case performance more than average performance, so I just now set it to "never".

On Ubuntu 14.04/amd64 I see:

$ cat /sys/kernel/mm/transparent_hugepage/enabled

[always] madvise never

I can also confirm that my Ubuntu 16.04.3 LTS (GNU/Linux 4.4.0-101-generic x86_64) droplet has the same setting.

The author opened a bug in Ubuntu about this here: https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1703742

It is in the process of being fixed (it should be set to madvise).

Quite curious, I'm running Ubuntu 16.04.3 LTS (4.11.0-14-generic x86_64) and have "madvise".

The parent said "droplet" so I assume Digital Ocean. Unless you've installed the host yourself, from scratch, you can't be sure the option hasn't been changed.

Makes me think that your setting is a default and his was set by Digital Ocean.

No, I have another Ubuntu 16.04 machine at home - same kernel version, same settings. He must have installed kernel 4.11 manually , because linux-image-generic currently pulls kernel 4.4.0-101-generic on 16.04; settings depend on kernel version.

Yes, I find it interesting that DO would change random kernel flags.

I suspect settings actually depend on kernel version: 4.4 -> 'always', 4.11 -> 'madvise'

Perhaps there are issues with 'madvise' in kernels prior to 4.11, so they chose 'always' rather than 'never'.