The 3-dimensional gyrokinetic PIC (particle-in-cell) code for MHD simulation, Gpic-MHD, was installed on SR16000 (“Plasma Simulator”), which is a scalar cluster system consisting of 8,192 logical cores. The Gpic-MHD code advances particle and field quantities in time. In order to distribute calculations over large number of logical cores, the total simulation domain in cylindrical geometry was broken up into N_DD-r × N_DD-z (number of radial decomposition times number of axial decomposition) small domains including approximately the same number of particles. The axial direction was uniformly decomposed, while the radial direction was non-uniformly decomposed. N_RP replicas (copies) of each decomposed domain were used (“particle decomposition”). The hybrid parallelization model of multi-threads and multi-processes was employed: threads were parallelized by the auto-parallelization and N_DD-r ×N_DD-z ×N_RP processes were parallelized by MPI (message-passing interface). The parallelization performance of Gpic-MHD was investigated for the medium size system of N_r × N_θ × N_z = 1025 × 128 × 128 mesh with 4.196 or 8.192 billion particles. The highest speed for the fixed number of logical cores was obtained for two threads, the maximum number of N_DD-z, and optimum combination of N_DD-r and N_RP. The observed optimum speeds demonstrated good scaling up to 8,192 logical cores.