Would NTFS allocation blocks of 16KB or 32KB make compile time faster in comparison to the default 4KB?
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3I can't imagine that would make much of a difference - disk block size is pretty far removed from compile speed. With the amount of caching a modern OS does, it seems unlikely to be significant.
The real answer, of course, can be found by measuring it. Getting similar conditions between different machines with different disk block sizes might be tricky, though.
My guess would be that disk fragmentation would be the biggest factor in determining compile speeds (that is, for a code base of decent size).
Dashogun is correct, at least in my experience. Larger projects / solutions create a lot of small, temporary files on the way to producing the final binary(ies). I find that if I defragment my disk once a week or so (even if the defragmenter does not recommend it) I do not see the performance degradation that I experience if I fail to do that.
As a corroborating factor, there are a couple of guys I work with that have the same experiences.