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[Colloquium] Petascale Computational Science on Roadrunner

October 3, 2008

Watch Colloquium: 

Quicktime file (718 Megs)
AVI file (570 Megs)

  • Date: Friday, October 3rd, 2008 
  • Time: 2 pm — 3:15 pm 
  • Place: ME 218

Timothy C. Germann
Deputy Group Leader of the Theoretical Chemistry & Molecular Physics Group (T-12) 

Abstract: I will describe the initial set of scientific applications and computational kernels that have been implemented on the hybrid Roadrunner supercomputer recently constructed by IBM for Los Alamos National Laboratory (LANL). Each Roadrunner “triblade” compute node consists of two AMD Opteron dual-core microprocessors and four PowerXCell 8i enhanced Cell microprocessors, typically utilized with a programming model of four MPI ranks (with one Opteron core and one Cell each) per node. I will describe our adventures first porting, and then drastically rewriting, a molecular dynamics code, SPaSM (Scalable Parallel Short-range Molecular dynamics), which is used for a wide range of scientific studies at LANL, ranging from fluid and materials dynamics to agent-based computational epidemiology. The computation of forces and updates of particle positions and velocities are performed on the Cells (each with one PPU and eight SPU cores), while the Opterons direct inter-rank communication and perform periodic I/O-heavy tasks including analysis, visualization, and checkpointing. The nearly perfect weak scaling measured for a standard Lennard-Jones pair potential benchmark yields 369 Tflop/s (double-precision) floating-point performance on the full Roadrunner system (3060 compute nodes), and is a finalist for the 2008 ACM Gordon Bell Prize to be announced at SC08 in November.

Bio: Timothy C. Germann is Deputy Group Leader of the Theoretical Chemistry & Molecular Physics Group (T-12) at Los Alamos National Laboratory (LANL). He earned Bachelor of Science degrees in Computer Science and in Chemistry from the University of Illinois in 1991, and a Ph.D. in Chemical Physics from Harvard University in 1995. Following a Research Fellowship in the Miller Institute for Basic Research in Science at UC Berkeley, where he developed parallel algorithms for quantum molecular (reactive) scattering theory, Tim joined LANL in 1997, where he has used large-scale classical molecular dynamics simulations to investigate shock, friction, detonation, and other materials dynamics issues using BlueGene/L, Roadrunner, and other NNSA supercomputer platforms. Along the way, he and his collaborators developed a large-scale epidemiological simulation model and applied it to assess mitigation strategies for outbreaks of either naturally emerging or intentionally released infectious diseases, including pandemic influenza. He has co-authored over 100 peer-reviewed scientific publications, and received a 1998 IEEE Gordon Bell Prize, 2005 and 2007 LANL Distinguished Performance Awards, a 2006 LANL Fellows’ Prize for Research, and a 2007 NNSA Defense Programs Award of Excellence.