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I am in the process of setting up new test servers to migrate to SQL Server 2017. For certain reasons I dont have the option to have a separate drive partition for just SQL binaries so my options are to put the SQL binaries on C:\ with default allocation unit size or G:\ with 64k allocation unit size along with the data files.

I would prefer to avoid C:\ and put the binaries on G:\ but am not sure if there would be any negative performance impact with them being on a disk with 64k format.

Is one better than the other or does it not really make any difference for the binaries?

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No it does not make any practical difference for the binaries. Unlike the data files, the binaries are largely loaded to memory on start up and not read from disk again during normal operation.

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