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For some new hardware I bought recently, I was almost lost in a maze recompiling the kernel and applying patches for SATA (libata) until I found out that the AMD-Xeon kernel on the Ubuntu repositories work just fine for Pentium-D processor.
The particular [:http://www.intel.com/cd/channel/reseller/asmo-na/eng/products/desktop/p…|Pentium-D I have] has a feature called EMT64, so 64-bit version of Ubuntu runs quite smoothly, with both cores getting detected.