Measuring the throughput is a very good overall measurement, unfortunately is made of many ingredients. Basically any detail of your system influences it (processor type, processor clock, disk, I/O connection, OS and version, compiler, optimization flags, software (ROOT), etc, etc.). So, unless you ensure that you run on the same hardware (processor, disk), and with the same compiler and software (ROOT) would allow you to say something about differences in the performance due to the operating system.