Affiliations: Department of Computer Science, Department of
Materials Science & Engineering, Department of Physics & Astronomy,
Department of Biomedical Engineering, University of Southern California, Los
Angeles, CA 90089, USA, and Concurrent Computing Laboratory for Materials
Simulations, Biological Computation and Visualization Center, Department of
Computer Science, Department of Physics & Astronomy, Louisiana State
University, Baton Rouge, LA 70803, USA. Tel.: +1 225 578 1342; Fax: +1 225 578
5855; E-mail: {nakano, kalia, priyav}@bit.csc.lsu.edu | Naval Oceanographic Office, Stennis Space Center, MS
39529, USA. E-mail: tjcamp@navo.hpc.mil | Department of Applied Sciences, Yamaguchi University,
Ube 755-8611, Japan. E-mail: ogata@po.cc.yamaguchi-u.ac.jp | Faculty of Integrated Arts and Sciences, Hiroshima
University, Higashi-Hiroshima 739-0046, Japan. E-mail:
shimojo@minerva.ias.hiroshima-u.ac.jp | IT Modeling and Simulation, NASA Ames Research Center,
Moffett Field, CA 94035-1000, USA. E-mail: saini@nas.nasa.gov
Abstract: A suite of scalable atomistic simulation programs has been developed
for materials research based on space-time multiresolution algorithms. Design
and analysis of parallel algorithms are presented for molecular dynamics (MD)
simulations and quantum-mechanical (QM) calculations based on the density
functional theory. Performance tests have been carried out on 1,088-processor
Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms
have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3
processors with parallel efficiency well over 90%. production-quality programs
also feature wavelet-based computational-space decomposition for adaptive load
balancing, spacefilling-curve-based adaptive data compression with user-defined
error bound for scalable I/O, and octree-based fast visibility culling for
immersive and interactive visualization of massive simulation data.
Keywords: parallel computing, molecular dynamics, variable-charge molecular dynamics, quantum mechanics, density functional theory, load balancing, data compression
