Optimization of Molecular Dynamics application for Intel Xeon Phi coprocessor
Amit Harode, Apaar Gupta, Benny Mathew, Nitin Rai · 2014
Molecular Dynamics (MD) is a computational technique with applicability in fields as diverse as material science, biomolecules and chemical physics. These applications are computationally intensive and massively parallel in nature and ideal candidate to exploit capabilities Intel Xeon Phi co-processor and Nvidia's Tesla GPU accelerators. In this work, we provide details of our experience in optimizing a molecular dynamics application on Xeon Phi. Xeon Phi is a product by Intel based on the Many Integrated Core Architecture. We exploit the 512 bit vector width of Xeon Phi through use of various techniques and achieve improved SIMD performance. We also implement shared memory model of OpenMP and reduce communication overheads between OpenMP threads by removal of reduction. These and other techniques described in the paper helped improve the applications performance on Xeon Phi by 322%.