You don't get something for nothing. In order to use hyperthreading there is an overhead cost to manage the multiple threads on the processor. If you are not using software that is optimized for hyperthreading then it is likely that it will run slower than if HT is disabled.
I see the same thing in my parallel data compression code. On a dual-processor machine with HT turned on (so 2 physical and 2 virtual CPUs), the software runs more slowly. When I turn it off, I see quite a speed boost.
otoh, a test workload on one of our server processes runs WAY faster with HT enabled on a dual xeon (so 4 virtual CPUs)... this load is a java message processing task which fires off a lot of threads that talk to a oracle databasse that does significant computational work (albeit not numerical) in oracle pl/sql stored procedures. there's also extensive disk IO primarily writes as oracle updates its indicies and writes its redo logs. reads are almost 100% cached.
however, this same workload runs twice as fast on a am64 Opteron server (actually, a quad opteron 2.2Ghz ran 4x faster than a dual xeon 2.8 2.2Ghz) which doesn't have any hyperthreading. so, this proves little.
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