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Does the UD Agent take advantage of multi-processor architecture/SMP?
Both UD.exe and the client apps are single thread applications so can only ever run a one CPU core. It can never use multiple cores at the same time (regardless of what windows is telling you).
It is the client apps (ligandfit, Rosetta) that do all the processing (99.9% of it in fact) and will use all available single core CPU time that it can get. It runs at the lowest priority level so it never interferes with any other apps on the system.
The UD.exe app runs at normal priority and only uses up CPU time if you have the apps graphical screen visible, when it is processing the result file for sending to UD or receiving new work. It also uses CPU time when a save occurs.
The P4D processor has Hyper-threading so to Windows it looks like you have 2 processors when in fact you still only have one. HT gives you 2 logical processors, with one having access to the integer unit (for running integer arithmatic) and the other having access to the floating point unit (FPU - to run floating point arithmatic) - remember there is still only one processor with one INT unit and one FPU.
Windows actually lies when using a HT CPU and will never show more than 50% for any application even though ligandfit is actually using 100% of the CPU because it uses the FPU for its calculations. Because HT is a poor mans SMP, Windows cannot accurately show the processor usage hence why you see different results at different times.