| 研究実績の概要 |
We made a substantial progress in developing the STEPS simulator and started developing the simulation of the whole Purkinje neuron. Continuing our effort in FY2016 for designing and implementing a highly scalable, parallel stochastic reaction-diffusion algorithm based on the Operation-Splitting method, in FY2017, we further extend our solution by implementing a parallel electric field (EField) solver using the PETSc library. The integration of TetOpSplit and PETSc EField solvers allows us to simulate complex models on an unprecedented scale. Using this, we finally reconstructed a complete Purkinje cell dendritic mesh of a million tetrahedrons from light microscope imaging data, and simulated our calcium burst model. Our pilot test suggested that the integrated TetOpSplit-PETSc EField solution is capable of dramatically reducing the simulation time compared to the traditional serial solution, even without any load balancing. This was released as STEPS 3.1.0 in June 2017, with subsequent releases of version 3.2.0 and 3.3.0 in October 2017 and April 2018, featuring a more flexible Cython API binding and other performance optimization. While with great success, we discovered in our pilot test that the operator splitting solution and the finite element EField solution demonstrated different scaling properties, which can be further optimized to achieve better speedup. This will be the focus in FY2018.
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