Efficient simulations of spiking neurons on parallel and distributed platforms: Towards large-scale modeling in computational neuroscience

摘要

Human brain communicates information by means of electro-chemical reactions and processes it in a parallel, distributed manner. Computational models of neurons at different levels of details are used in order to make predictions for physiological dysfunctions. Advances in the field of brain simulations and brain computer interfaces have increased the complexity of this modeling process. With a focus to build large-scale detailed networks, we used high performance computing techniques to model and simulate the granular layer of the cerebellum. Neuronal firing patterns of cerebellar granule neurons were modeled using two mathematical models Hodgkin-Huxley (HH) and Adaptive Exponential Leaky Integrate and Fire(AdEx). The performance efficiency of these modeled neurons was tested against a detailed multi-compartmental model of the granule cell. We compared different schemes suitable for large scale simulations of cerebellar networks. Large networks of neurons were constructed and simulated. Graphic Processing Units (GPU) was employed in the pleasantly parallel implementation while Message Passing Interface (MPI) was used in the distributed computing approach. This allowed to explore constraints of different parallel architectures and to efficiently load balance the tasks by maximally utilizing the available resources. For small scale networks, the observed absolute speedup was 6X in an MPI based approach with 32 processors while GPUs gave 10X performance gain compared to a single CPU implementation. In large networks, GPUs gave approximately 5X performance gain in processing time compared to the MPI implementation. The results enabled us to choose parallelization schemes suitable for large-scale simulations of cerebellar circuits. We are currently extending the network model based on large scale simulations evaluated in this paper and using a hybrid ??? heterogeneous MPI based multi-GPU architecture for incorporating millions of cerebellar neurons for assessing physiol- gical disorders in such circuits.