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The optimization of the central region structure of the cyclotron requires a tedious iterative procedure using a substantial amount of the particle tracking in the machine. The problem becomes even more complicated when the beam space charge effects should be taken into account. The solution of the problem was attempted via upgrade of the recently developed computer code CBDA [1] based on the beam dynamics calculation by the NVIDIA CUDA parallel computing architecture. The main part of calculation was performed without application of the CPU, and only a video card with GPU of about 100-200 processors was used. An application of the video card with the GPU instead of multi-processor computer is very cost effective solution in this case. References [1] E.E. Perepelkin and S.B. Vorozhtsov. ’CBDA - Cyclotron Beam Dynamics Analysis code’. In Proc.: The XXI Russian Accelerator Conference (RuPAC2008), Zvenigorod, Russia, September 28 - October 3, 2008, p.40-42.