GPU. Energy Consumption and Acceleration of GPU of Molecular Dynamics Simulation. TAKURO UDAGAWA 1 and MASAKAZU SEKIJIMA 2, 3

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1 GPU 1 2, 3 GPU Newton GPU CPU Energy Consumption and Acceleration of GPU of Molecular Dynamics Simulation TAKURO UDAGAWA 1 and MASAKAZU SEKIJIMA 2, 3 Molecular dynamics simulations are widely used for simulating the motion of molecules in order to gain a deeper understanding of chemical reactions, fluid flow, phase transitions, and other physical phenomena due to molecular interactions. However, these simulations require huge computer resources. In addition, the problem of energy consumption must be solved. Recently, GPGPU has attracted attention as a possible solution to these problems. In this paper, we performed molecular dynamics simulations on a CPU and GPU, and compare calculation time, power consumption and energy consumption results between them. 1 Department of Computer Science, Tokyo Institute of Technology 2 Global Scientific Information and Computing Center, Tokyo Institute of Technology 3 Department of Computer Science, Tokyo Institute of Technology 1. (Molecular Dynamics; MD) Newton 1)2) MD femto nano micro MD MD 4)3) GPU(Graphics processing units) GPU GPU GPGPU(general purpose computation on graphics processing units) GPU 6) 7) 8) GPU Nebulae NVIDIA GPU Tesla C TOP ) TSUBAME2.0 NVIDIA Tesla M2050 GPU IT 5) GPU 1 c 2010 Information Processing Society of Japan

2 CPU CPU 2. femto ( 1 ) ( 2 ) ( 3 ) ( 4 ) 1-3 ( 5 ) ( 6 ) ( 7 ) 1-6 (1) [ ( ) 12 ( ) ] 6 σ σ ϕ(r ij) = 4ε r ij r ij ij r ij i j ε σ Verlet Verlet (2)(3) r i(t +) = 2r i(t) r i(t ) + a i(t)( t) 2 (2) v i(t) = 1 [ri(t+) ri(t )] (3) 2 t (4) (5) (6) Φ = ϕ(r ij ) (4) i<j (1) K = 1 2 miv2 i (5) T = 2K (6) 3k B N m i i v i i k B N 3. GPU 3.1 NVIDIA CUDA GPU Brook+ 9),ATI Stream 11) C NVIDIA CUDA CUDA NVIDIA GPU G80 GT200 Fermi NVIDIA GPU SM(Streaming Multiprocessor) SM CUDA SM GPU SM GPU Fermi GTX SM SM 32 CUDA 480 CUDA CUDA CPU C GPU GPU GPU CPU GPU CPU GPU GPU CUDA ( 1) CUDA SM SM 32 14) 2 c 2010 Information Processing Society of Japan

3 potential energy kinetic energy kernel function2 1 CUDA memory (atoms data) 3.2 GPU GPU CPU GPU GPU GPU Mahsan Rofouei separate convolutions LEAP-Server GPU GPU 12) GPU 1 Nebulae TOP500 2 Nebulae Green ) Green500 MFLOPS/watt TOP500 1 Jugar Green CUDA CUDA ( 1 ) GPU ( 2 ) CPU GPU ( 3 ) ( 4 ) ( 5 ) GPU CPU ( 6 ) GPU kernel function1 th.1 th.2 th.3 th.n 2 GPU ( 2) CPU CPU Intel Core i GHz CPU 4 256KB L2 8MB L3 GB DDR3 SDRAM GPU NVIDIA GT240 GT CUDA OS Ubuntu9.04 CUDA c 2010 Information Processing Society of Japan

4 MD CPU GPU SYSTEM ARTWARE WATT-HOUR METER SHW3A NEV 6. 1, 3 4 CPU 8 CPU GPU CPU-GPU GPU 64 GPU CPU MD GPU 1 results atoms value CPU GPU sec watt joule sec watt joule sec watt joule sec watt joule GPU CPU elapsed calculation time energy consumption(j) number of atoms CPU GPU CPU GPU number of atoms 4 4 c 2010 Information Processing Society of Japan

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