SESSION: Gordon Bell I
CHAIR:
TIME: Wednesday 11/20 1:30-3:00
ROOM: 309-310

1. pap146
TITLE: A 29.5 Tflops simulation of planetesimals in Uranus-Neptune region on GRAPE-6
AUTHORS: Junichiro Makino (Department of Astronomy, School of Science, University of Tokyo)
Eiichiro Kokubo (National Astronomical Observatory of Japan)
Toshiyuki Fukushige (Department of General System Studies, College of Arts and Sciences, University of Tokyo)
Hiroshi Daisaka (Department of Astronomy, School of Science, University of Tokyo)

ABSTRACT:
As an entry for the 2002 Gordon Bell performance prize, we report the performance achieved on the GRAPE-6 system for a simulation of the early evolution of the protoplanet-planetesimal system of the Uranus-Neptune region. GRAPE-6 is a special-purpose computer for astrophysical N-body calculations. The present configuration has 2048 custom pipeline chips, each containing six pipeline processors for the calculation of gravitational interactions between particles. Its theoretical peak performance is 63.4 Tflops. The actual performance obtained was 29.5 Tflops, for a simulation of the early evolution of outer Solar system with 1.8 million planetesimals and two massive protoplanets.

2. pap216
TITLE: Salinas: A Scalable Software for High-Performance Structural and Solid Mechanics Simulations
AUTHORS: Manoj Bhardwaj (Sandia National Labs)
Kendall Pierson (Sandia National Labs)
Garth Reese (Sandia National Labs)
Tim Walsh (Sandia National Labs)
David Day (Sandia National Labs)
Ken Alvin (Sandia National Labs)
James Peery (Sandia National Labs)
Charbel Farhat (Univeristy of Colorado at Boulder)
Michel Lesoinne (University of Colorado at Boulder)

ABSTRACT:
We present Salinas, a scalable implicit software application for the finite element static and dynamic analysis of complex structural real-world systems. This relatively complete engineering software with more than 100,000 lines of C++ code and a long list of users sustains 292.5 Gflop/s on 2,940 ASCI Red processors, and 1.16 Tflop/s on 3,375 ASCI White processors.

3. pap277
TITLE: NAMD: Biomolecular Simulation on Thousands of Processors
AUTHORS: James C. Phillips (Beckman Institute, University of Illinois at Urbana-Champaign)
Gengbin Zheng (Department of Computer Science and Beckman Institute, University of Illinois at Urbana-Champaign)
Sameer Kumar (Department of Computer Science and Beckman Institute, University of Illinois at Urbana-Champaign)
Laxmikant V. Kale (Department of Computer Science and Beckman Institute, University of Illinois at Urbana-Champaign)

ABSTRACT:
NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demonstrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (order N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place of MPI by the Charm++/Converse parallel runtime system.