The design and implementation of an FPGA core that parallelises all the necessary operations to compute the non-bonded interactions in a MD simulation with the purpose of accelerating the LAMMPS MD software is presented in this paper. Our MD processor core comprised of 4 identical pipelines working independently in parallel to evaluate the non-bonded potentials, forces and virials was implemented on the nodes of a FPGA-based supercomputer, namely Maxwell. Implementing our FPGA core on multiple nodes of Maxwell allowed us to produce a special-purpose parallel machine for the hard-ware acceleration of MD simulations. The timing performance figures of this machine for the pairwise LJ and short-range Coulombic (via PPPM) interaction computations in the MD simulations of the solvated Rhodopsin protein systems show performance gains over the pure software implementation by factors of up to 14 on two or more nodes of the Maxwell machine.
|Title of host publication||Proceedings of the 2011 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2011|
|Number of pages||8|
|Publication status||Published - 29 Jul 2011|
|Event||2011 NASA/ESA Conference on Adaptive Hardware and Systems - San Diego, United States|
Duration: 6 Jun 2011 → 9 Jun 2011
|Conference||2011 NASA/ESA Conference on Adaptive Hardware and Systems|
|Period||6/06/11 → 9/06/11|