GPU Acceleration of Nonbonded Forces for Molecular Dynamics Simulation
Cheng Juan · Computer Engineering and Science · 2009
The most costly computation required by molecular dynamics(MD) is the calculation of non-bonded forces.This paper presents two algorithms based on CUDA and Brook+ to accelerate the calculation of non-bonded forces and then examines them on two popular GPUs of NVIDIA and AMD.The algorithms enable fine-grained task decomposition and spatial decomposition of forces that map efficiently to the compute units of GPU.They also present optimization methods such as use of shared memory between threads and strip-mined.We then test our implementations for 432 thousand atoms.Our code executed on Tesla C1060 runs 6.5 times faster than the original application running on single core of Intel Intel Xeon 2.6GHZ CPU,while on HD4870 it runs 4.8 times faster.