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Neuroscience is witnessing increasing knowledge about the anatomy and electrophysiological properties of neurons and their connectivity, leading to an ever increasing computational complexity of neural simulations. At the same time, a rather radical change in personal computer technology emerges with the establishment of multi-cores: high-density, explicitly parallel processor architectures for both high performance as well as standard desktop computers. This work introduces strategies for the parallelization of biophysically realistic neural simulations based on the compartmental modeling technique and results of such an implementation, with a strong focus on multi-core architectures and automation, i.e. user-transparent load balancing.

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The efficient use of multicore architectures for sparse matrixvector multiplication (SpMV) is currently an open challenge. One algorithm which makes use of SpMV is the maximum likelihood expectation maximization (MLEM) algorithm. When using MLEM for positron emission tomography (PET) image reconstruction, one requires a particularly large matrix. We present a new storage scheme for this type of matrix which cuts the memory requirements by half, compared to the widelyused compressed sparse row format. For parallelization we combine the two partitioning techniques recursive bisection and striping. Our results show good load balancing and cache behavior. We also give speedup measurements on various modern multicore systems.

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