Atrial fibrillation Atrial flutter Atrial tachycardia AV nodal reentrant tachycardia AV reentrant tachycardia Bigemin Premature ventricular contraction.

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Presentation transcript:

Atrial fibrillation Atrial flutter Atrial tachycardia AV nodal reentrant tachycardia AV reentrant tachycardia Bigemin Premature ventricular contraction Ventricular tachycardia Ventricular fibrillation Bundle branch black Heart block

GPU CNC CUBLAS Reaction Diffusion

33 state + 1 voltage + 1 current variables / node update per time step Transmembrane voltage (V m ) and current (I tot ) output for diffusion phase

OpenNL Sparse Matrix interface with CNC ELL support Exposed Sparse Matrix Vector Multiply in CNC Conjugate Gradient (CG) handled by CNC CUBLAS for vector operations

Time Step 0 ms Time Step 40 ms 8000 iterations

Large number of registers needed per thread per calculation Frequent use of slow math functions Limited data storage per thread Tesla architecture with more registers MPI to better distribute data load Hardware math functions at a cost of precision Size of the Laplacian matrices, 32K nodes equals about a 4GB matrix Using libraries for sparse matrix support, compress 32K x 32K matrix to 16 MB storage Loss of precision and numerical stability by using single precision floating point numbers

Rabbit model: 50 ms activity, timestep 20 μs, 425,000 nodes run time: 3316 seconds Rabbit model: 50 ms activity, timestep 20 μs, 425,000 nodes run time: 3316 seconds Carp (MPI, PETSc) Rabbit model: 30 ms of activity, 3 million nodes run time: 13 hours Rabbit model: 30 ms of activity, 3 million nodes run time: 13 hours Human model: 600 ms activity, time step 10 μs, 55 million nodes run time: 2 days Human model: 600 ms activity, time step 10 μs, 55 million nodes run time: 2 days Mouse, rabbit model, GPU and GPU/MPI hybrid version: membrane current computation, time step 25 μs, 10e4 - 10e6 nodes run time: seconds Mouse, rabbit model, GPU and GPU/MPI hybrid version: membrane current computation, time step 25 μs, 10e4 - 10e6 nodes run time: seconds CHASTE(MPI,PETSc) Potse, Dubé, Vinet, Cardinal (OpenMP)