Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL

Molecular dynamics (MD) simulations are very important to study physical properties of the atoms and molecules. However, a huge amount of processing time is required to simulate a few nano-seconds of an actual experiment. Although the hardware acceleration using FPGAs provides promising results, huge design time and hardware design skills are required to implement an accelerator successfully. In this paper, we propose an FPGA accelerator designed using C-based OpenCL. We achieved over 4.6 times of speed-up compared to CPU-based processing, by using only 36% of the Stratix V FPGA resources. Maximum of 18.4 times speed-up is possible by using 80% of the FPGA resources.

[1]  Haruki Nakamura,et al.  Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions. , 2013, Journal of chemical theory and computation.

[2]  Md. Ashfaquzzaman Khan.  Scalable Molecular Dynamics Simulation Using FPGAs and Multicore Processors , 2013 .

[3]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[4]  Eunjung Cho,et al.  An FPGA Design to Achieve Fast and Accurate Results for Molecular Dynamics Simulations , 2007, ISPA.

[5]  Masanori Hariyama,et al.  OpenCL-Based Design of an FPGA Accelerator for Phase-Based Correspondence Matching , 2015 .

[6]  Server Kasap,et al.  Parallel Processor Design and Implementation for Molecular Dynamics Simulations on a FPGA-Based Supercomputer , 2012, J. Comput..

[7]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[8]  Peter V. Coveney,et al.  Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS , 2004, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[9]  John L. Klepeis,et al.  Anton, a special-purpose machine for molecular dynamics simulation , 2007, ISCA '07.

[10]  Yu Cao,et al.  Throughput-Optimized OpenCL-based FPGA Accelerator for Large-Scale Convolutional Neural Networks , 2016, FPGA.

[11]  J. P. Grossman,et al.  Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer , 2014, SC14: International Conference for High Performance Computing, Networking, Storage and Analysis.

[12]  M.G.B. Drew,et al.  The art of molecular dynamics simulation , 1996 .

[13]  J. Xu.  OpenCL – The Open Standard for Parallel Programming of Heterogeneous Systems , 2009 .

[14]  Federico D. Sacerdoti,et al.  Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters , 2006, ACM/IEEE SC 2006 Conference (SC'06).