Overheads in Accelerating Molecular Dynamics Simulations with GPUs

Molecular Dynamics (MD) simulation requires huge computational power, as each atom interacts with the others by long range forces such as the Coulomb or van der Waals forces. Recently, a video game computer, such as SONY PLAYSTATION 3 (PS3) or NVIDIApsilas Graphics Processing Unit (GPU) has become a candidate hardware for accelerating MD simulations as well as an MDGRAPE-3 special-purpose computer for their better performance than current CPU of the PC, and also for their cost-effectiveness. Especially the latest GPU has much more peak performance than a CPU of the PC or an MDGRAPE-3, though a GPU has much more overheads in accelerating MD simulations. When the number of particles is small or the calculation kernel becomes complicated, the performance of the GPU drops dramatically as low as that of the MDGRAPE-3. However, the acceleration ratio of the GPU and the PS3 per cost exceeds that of the MDGRAPE-3.