Porting the GROMACS Molecular Dynamics Code to the Cell Processor

The Cell processor offers substantial computational power which can be effectively utilized only if application design and implementation are tuned to the Cell architecture. In this paper, we examine application characteristics which facilitate efficient use of the Cell processor, and those which present obstacles to it. Moreover, we consider possible solutions designed to mitigate inefficiencies. The target application in our study is the GROMACS molecular dynamics package. We have accelerated the most-often used compute-intensive kernel while maintaining the constraints imposed by the structure of the surrounding program. The significant contribution of this paper is the consideration of the kernel in the context of a complex end-to-end application, with irregular data and code patterns, rather than an isolated kernel code. For this challenging scenario, our results show a 2X speedup versus hand-tuned VMX/SSE code running on high-end PowerPC and x86 uniprocessor machines.