If a Q# operation does not use qubits or quatum specific gates, will then the CLR generate bytecode that will be executed by the CPU and not the QPU(quantum processor)?
How does CLR compile Q# code that uses or does not make use of qubits?
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Yes, exactly. The Q# compiler translates the purely classical parts of your code into C#, which gets compiled (by the C# compiler) into standard .NET MSIL, JITed by the .NET Core runtime, and executed on a normal CPU.