ECC memory scrubbing is best done by the hardware. The AMD 760MP and 760MPX chip sets do this, as does the memory controller built into the Opteron and Athlon64. I'm not sure about scrubbing on Intel-based hardware (though the first system I ever used with ECC memory scrubbing was an Intel iAPX-432 system in the early 1980s).
If the hardware does not have scrubbing support, it can be done by a user level process with no special kernel support needed, but it will thrash the data cache. You should be able to scrub slowly enough that the overhead is minimal, while still maintaining the benefit of scrubbing.
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