Disabling HT requires BIOS support. Some OEMs provide you with an option to disable HT, but it sounds like this option is not available for the Toshiba* Tecra S11 platform. Do you have the lastest BIOS from Toshiba?
I am not aware of any application that runs better with HT disabled rather than enabled, and I doubt that disabling HT would address the kind of performance difference you are seeing. I think BIOS question and the performance issue is something you may need to bring up with Toshiba.
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werez Try setting the affinity of the software to use one thread per core, perhaps by using Taskmanager. This should give you a good idea of how the software would run without HT.