I have taken the CPU out of the system and found it is an SL6PE.

http://www.cpu-world.com/sspec/SL/SL6PE.html

Although the CPU shows the HT flag, it actually does not support
hyperthreading.

I installed an SL6S5. Since installing, hyperthreading is enabled
whether or not I add ht=on in the kernel boot parameters.

It appears the ht flag in /proc/cpuinfo is not a reliable way to
determine whether a CPU supports hyperthreading.

I'll mark the bug as invalid.

** Changed in: linux (Ubuntu)
       Status: Confirmed => Invalid

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Can't enable Hyper-Threading
https://bugs.launchpad.net/bugs/277085
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