SCHEDULE: NOV 10-16, 2012
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Neural Circuit Simulation of Hodgkin-Huxley Type Neurons Toward Peta Scale Computers
SESSION: ACM Student Research Competition Poster Session
EVENT TYPE: ACM Student Research Competition
TIME: 5:15PM - 7:00PM
SESSION CHAIR: Torsten Hoefler
AUTHOR(S):Daisuke Miyamoto
ROOM:East Entrance
ABSTRACT:
We ported and optimized simulation environment "NEURON" on K computer to simulate a insect brain as multi-compartment Hodgkin-Huxley type model.
To use SIMD units of SPARC64VIIIfx (CPU of K computer), we exchanged the order of the compartment loop and the ion channel loop and apply sector caches. These tuning improved single core performance 340 MFLOPS/core to 1080 MFLOPS/core (about 7% efficiency).
Spike exchange method of NEURON (MPI_Allgather) demands large amount of time in case of 10,000 cores or more and simple asynchronous point-to-point method (MPI_Isend) is not effective too, because of a large number of function calls and long distance of interconnect pathway. To tackle these problems, we adopted MPI/OpenMP hybrid parallelization to reduce interconnect communications and we developed a program to optimize location of neurons on calculation nodes in the 3D torus network. As a these results, we preliminary obtained about 70 TFLOPS with 196,608 CPU cores.
Chair/Author Details:
Torsten Hoefler (Chair) - ETH Zurich
Daisuke Miyamoto - University of Tokyo
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