1. A method for compiling and executing an application in a system including a Central Processing Unit (CPU) and a Graphic Processing Unit (GPU), the method comprising: receiving a request for compiling the application, the application including CPU source code and GPU source code; compiling the CPU source code into CPU machine code, and compiling the GPU source code into a GPU virtual instruction; generating an execution file by linking the CPU machine code and the GPU virtual instruction in response to the request, the execution file including a virtual section including information relating to CPU execution time and GPU execution time; receiving a request for executing the execution file; identifying whether to execute the execution file on the CPU or the GPU based on the information relating to the CPU execution time and the GPU execution time; and executing the execution file on one of the CPU and the GPU based on a result of identifying whether to execute the execution file on the CPU or the GPU, and wherein the executing the execution file further comprises translating the GPU virtual instruction into GPU machine code, and inserting the GPU machine code into the execution file in response to the request for executing the execution file; and executing the CPU machine code and the GPU machine code.