Analytic Performance Modeling and Analysis of Detailed Neuron Simulations

Big science initiatives are trying to reconstruct and model the brain by attempting to simulate brain tissue at larger scales and with increasingly more biological detail than previously thought possible. The exponential growth of parallel computer performance has been supporting these developments, and at the same time maintainers of neuroscientific simulation code have strived to optimally and efficiently exploit new hardware features. Current state of the art software for the simulation of biological networks has so far been developed using performance engineering practices, but a thorough analysis and modeling of the computational and performance characteristics, especially in the case of morphologically detailed neuron simulations, is lacking. Other computational sciences have successfully used analytic performance engineering and modeling methods to gain insight on the computational properties of simulation kernels, aid developers in performance optimizations and eventually drive co-design efforts, but to our knowledge a model-based performance analysis of neuron simulations has not yet been conducted. We present a detailed study of the shared-memory performance of morphologically detailed neuron simulations based on the Execution-Cache-Memory (ECM) performance model. We demonstrate that this model can deliver accurate predictions of the runtime of almost all the kernels that constitute the neuron models under investigation. The gained insight is used to identify the main governing mechanisms underlying performance bottlenecks in the simulation. The implications of this analysis on the optimization of neural simulation software and eventually co-design of future hardware architectures are discussed. In this sense, our work represents a valuable conceptual and quantitative contribution to understanding the performance properties of biological networks simulations.Comment: 18 pages, 6 figures, 15 table

Entangled histories/touching tales - eine transdisziplinäre Annäherung

Tagungsbericht: Veranstalter: Exzellenzcluster "Die Herausbildung normativer Ordnungen", Goethe-Universität Frankfurt am Main. Datum, Ort: 17.02.2010, Frankfurt am Mai

Neue Hilfsmittel zur amerikanischen Walfanggeschichte

The article introduces two collections of data on the history of whaling in America. The first lists all hitherto verified American whaling expeditions, the second more than 120,000 sailors who departed on vessels from New Bedford. Both resources are available in the Internet free of charge

Exploring Liquid Computing in a Hardware Adaptation : Construction and Operation of a Neural Network Experiment

Future increases in computing power strongly rely on miniaturization, large scale integration, and parallelization. Yet, approaching the nanometer realm poses new challenges in terms of device reliability, power dissipation, and connectivity - issues that have been of lesser concern in today's prevailing microprocessor implementations. It is therefore necessary to pursue the research on alternative computing architectures and strategies that can make use of large numbers of unreliable devices and only have a moderate power consumption. This thesis describes the construction of an experiment dedicated to exploring silicon adaptations of artificial neural network paradigms for their general applicability, power efficiency, and fault-tolerance. The presented setup comprises peripheral electronics, programmable logic, and software to accommodate a mixed-signal CMOS microchip implementing a flexible perceptron with 256 McCulloch-Pitts neurons. This neural network experiment is used to explore a recent strategy that allows to access the power of recurrent network topologies. While it has been conjectured that this liquid computing is suited for hardware implementations, this first time adaptation to a CMOS neural network affirms this claim. Not only feasibility but also tolerance to substrate variations and robustness to faults during operation are demonstrated

Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer

For neural network simulations on parallel machines, interprocessor spike communication can be a significant portion of the total simulation time. The performance of several spike exchange methods using a Blue Gene/P (BG/P) supercomputer has been tested with 8–128 K cores using randomly connected networks of up to 32 M cells with 1 k connections per cell and 4 M cells with 10 k connections per cell, i.e., on the order of 4·1010 connections (K is 1024, M is 10242, and k is 1000). The spike exchange methods used are the standard Message Passing Interface (MPI) collective, MPI_Allgather, and several variants of the non-blocking Multisend method either implemented via non-blocking MPI_Isend, or exploiting the possibility of very low overhead direct memory access (DMA) communication available on the BG/P. In all cases, the worst performing method was that using MPI_Isend due to the high overhead of initiating a spike communication. The two best performing methods—the persistent Multisend method using the Record-Replay feature of the Deep Computing Messaging Framework DCMF_Multicast; and a two-phase multisend in which a DCMF_Multicast is used to first send to a subset of phase one destination cores, which then pass it on to their subset of phase two destination cores—had similar performance with very low overhead for the initiation of spike communication. Departure from ideal scaling for the Multisend methods is almost completely due to load imbalance caused by the large variation in number of cells that fire on each processor in the interval between synchronization. Spike exchange time itself is negligible since transmission overlaps with computation and is handled by a DMA controller. We conclude that ideal performance scaling will be ultimately limited by imbalance between incoming processor spikes between synchronization intervals. Thus, counterintuitively, maximization of load balance requires that the distribution of cells on processors should not reflect neural net architecture but be randomly distributed so that sets of cells which are burst firing together should be on different processors with their targets on as large a set of processors as possible