NUMA support did strike me as a possible cause.

I thought that L2 caches on the Opteron communicated by I assume by your response the Opteron memory controller doesn't allow cache propagation, instead invalidates the cache entries read (assuming again the write entries are handled differently).

Menezes, Evandro wrote:
Honza,
Well, rather than unstable, they seems to be more memory layout
sensitive I would say. (the differences are more or less reproducible,
not completely random, but independent on the binary itself. I can't
think of much else than memory layout to cause it).  I always wondered
if things like page coloring have chance to reduce this noise, but I
never actually got around trying it.

You didn't mention the processors in your systems, but I wonder if they are dual-core.  If so, 
perhaps it's got to do with the fact that each K8 core has its own L2, whereas C2 chips have a 
shared L2.  Then, try preceding "runspec" with "taskset 0x02" to avoid the 
process from hopping between cores and finding cold caches (though the kernel strives to stick a 
process to a single core, it's not perfect).

HTH


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