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wasn't hyperthreading disabled on recent BSD-based oses due to this horrendous potential security hole?
No, someone pointed out on the Linux kernel mailing list, that there is a small, but theoreticaly possible security issue if a trusted and untrusted process are running concurently on a hyperthreaded CPU.
It was shown, that the untrusted process would be able to get clues about what the trusted process was doing, by comparing the cache latency of different memory accesses, as clearly if the trusted process had allready put some data in the CPU's cache, then the untrusted process would get it much faster. This could be used to leak confidental data in a shared hosting environment for example.
Clearly the same issue would apply to dual core CPUs where both cores share the same L2 Cache, such as current Athlon X2 designs.
Having said all that, this is all theoretical, and as far as I am aware, no one has produced any exploit code to demonstrate the issue.
There was talk a few months back about adding hooks to Linux, to allow security sensitive processes such as password or login, to request that no untrusted processes be scheduled on the same CPU while they run, but as far as I am aware, this has not been implemented.