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From what I can hear the only issue with software based tagging is that you have to make sure you control all the allocation systems? (I.E. so they don't malloc(huge) and then do internal things to it?) Or did I get confused?
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The only issue in what sense? Hardware memory tagging won't be able to handle the custom allocators (malloc(huge)) properly too. But there will be no need to rebuild the code itself, you only need to change allocator.
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