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Can you pass it in through the CFLAGS environment variable as is? (Ugly, but I think CMake claims to respect that variable.)

This appears to work. I have pushed a change to metis.py to do this define the Mac. We should eventually have BuildSystem check for __thread but I'm too lazy to do that today.

This doesn't work on cray, it seems. I went ahead and reverted Barry's change while adding support for "cflags=blah."