Paper Citing NAMD - Abstract
Bhatele, Abhinav; Wesolowski, Lukasz; Bohm, Eric; Solomonik, Edgar; Kale, Laxmikant V.
Understanding Application Performance via Micro-benchmarks on Three Large Supercomputers: Intrepid, Ranger and Jaguar
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 24:411-427, NOV 2010
The emergence of new parallel architectures presents new challenges for application developers. Supercomputers vary in processor speed, network topology, interconnect communication characteristics and memory subsystems. This paper presents a performance comparison of three of the fastest machines in the world: IBM's Blue Gene/P installation at ANL (Intrepid), the SUN-Infiniband cluster at TACC (Ranger) and Cray's XT4 installation at ORNL (Jaguar). Comparisons are based on three applications selected by NSF for the Track 1 proposal to benchmark the Blue Waters system: NAMD, MILC and a turbulence code, DNS. We present a comprehensive overview of the architectural details of each of these machines and a comparison of their basic performance parameters. Application performance is presented for multiple problem sizes and the relative performance on the selected machines is explained through micro-benchmarking results. We hope that insights from this work will be useful to managers making buying decisions for supercomputers and application users trying to decide on a machine to run on. Based on the performance analysis techniques used in the paper, we also suggest a step-by-step procedure for estimating the suitability of a given architecture for a highly parallel application.
