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GPGPU Accelerated Cardiac Arrhythmia Simulations

GPGPU Accelerated Cardiac Arrhythmia Simulations. Wei Wang 1 , H. Howie Huang 2 , Matthew Kay 2 and John Cavazos 1 University of Delaware The George Washington University. Motivation. Cardiac arrhythmia ~300,000 people/year in the US Cure Image-guided ablation therapy

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GPGPU Accelerated Cardiac Arrhythmia Simulations

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  1. GPGPU Accelerated Cardiac Arrhythmia Simulations Wei Wang1, H. HowieHuang2, Matthew Kay2 and John Cavazos1 University of Delaware The George Washington University

  2. Motivation • Cardiac arrhythmia • ~300,000 people/year in the US • Cure • Image-guided ablation therapy • Simulation improves efficacy • Problem • Sequential execution of simulation too slow!

  3. Simulation: Cardiac Model

  4. Acceleration Concept N11 N21 N31 Sequential (Running on CPU) Parallel (Enabled by GPGPUs) N12 N22 N32 N13 N23 N33

  5. Acceleration Tool—GPU • Example: NVIDIA Tesla C1060 • 240 Processing Elements • Massively parallel multithreaded • Up to 30720 active threads CPU GPU

  6. Acceleration Considerations • SIMD • Large Matrix • No (Few) Temporal Data Dependency • Acceleration Command—CUDA • Using Atomic Functions*

  7. GPU Acceleration for (Xstep=1;Xstep<Nx+1;++Xstep){ for (Ystep=1;Ystep<Ny+1;++Ystep){ stimulate(); //apply stimulating current brgates(); // update gating equations brcurrents(); // update currents mdiff(); // update diffusion terms } // end Ystep loop } // end Xstep loop bcs(); // apply boundary conditions GPU_ GPU_ GPU_ GPU_

  8. Simulation Results Point Stimulation Electrical Rotor Simulation

  9. Point Simulation Results Speedup (normalized to seq perf) Matrix Sizes

  10. Thank you! Wei Wang weiwang@udel.edu http://www.cis.udel.edu/~wwang Please consider GPGPU

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