SCHEDULE: NOV 12-18, 2011

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3D Tixels: A Highly Efficient Algorithm for GPU/CPU-Acceleration of Molecular Dynamics on Heterogeneous Parallel Architectures

SESSION: Research Poster Reception

EVENT TYPE: ACM Student Research Competition Poster, Poster, Electronic Poster

TIME: 5:15PM - 7:00PM

SESSION CHAIR: Bernd Mohr

AUTHOR(S):Szilárd Páll, Berk Hess, Erik Lindahl

ROOM:WSCC North Galleria 2nd/3rd Floors

ABSTRACT:
Several GPU-based algorithms have been developed to accelerate biomolecular simulations, but although they provide benefits over single-core implementations, they have not been able to beat state-of-the art SIMD CPU implementations (e.g. GROMACS) running on modern hardware with 12-24 cores, not to mention achieve efficient scaling. Here, we present a new heterogeneous acceleration approach that utilizes all CPU/GPU resources efficiently. A novel fixed-particle-number sub-cell algorithm makes it possible to combine neutral-territory domain decomposition in GROMACS with CUDA nonbonded kernels that achieve 60% work-efficiency, 1.5IPC and 95% cache utilization. The algorithm is intrinsically future-proof since cell sizes can be adapted to future hardware. Lattice summation is simultaneously handled with an OpenMP-based CPU implementation that balances the load between CPU/GPU domains. We achieve threefold speedup compared to GROMACS running on all cores of a workstation, which to the best of our knowledge makes this the fastest GPU molecular dynamics implementation presented to date.

Chair/Author Details:

Bernd Mohr (Chair) - Juelich Supercomputing Centre

Szilárd Páll - KTH Royal Institute of Technology

Berk Hess - KTH Royal Institute of Technology

Erik Lindahl - KTH Royal Institute of Technology

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