Fast analysis of molecular dynamics trajectories with graphics processing units - Radial distribution function histogramming

The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU’s memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used muc...

• Type: Journal
• Year: 2011
• Where: JCPHY
• Authors: Benjamin G. Levine, John E. Stone, Axel Kohlmeyer
• Keywords: Intel Xeon, JCPHY 2011, Memory Hierarchy, Multithreaded Implementation