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

Exploring performance and power properties of modern multicore chips via simple machine models

Modern multicore chips show complex behavior with respect to performance and power. Starting with the Intel Sandy Bridge processor, it has become possible to directly measure the power dissipation of a CPU chip and correlate this data with the performance properties of the running code. Going beyond a simple bottleneck analysis, we employ the recently published Execution-Cache-Memory (ECM) model to describe the single- and multi-core performance of streaming kernels. The model refines the well-known roofline model, since it can predict the scaling and the saturation behavior of bandwidth-limited loop kernels on a multicore chip. The saturation point is especially relevant for considerations of energy consumption. From power dissipation measurements of benchmark programs with vastly different requirements to the hardware, we derive a simple, phenomenological power model for the Sandy Bridge processor. Together with the ECM model, we are able to explain many peculiarities in the performance and power behavior of multicore processors, and derive guidelines for energy-efficient execution of parallel programs. Finally, we show that the ECM and power models can be successfully used to describe the scaling and power behavior of a lattice-Boltzmann flow solver code.Comment: 23 pages, 10 figures. Typos corrected, DOI adde

Engineering Crowdsourced Stream Processing Systems

A crowdsourced stream processing system (CSP) is a system that incorporates crowdsourced tasks in the processing of a data stream. This can be seen as enabling crowdsourcing work to be applied on a sample of large-scale data at high speed, or equivalently, enabling stream processing to employ human intelligence. It also leads to a substantial expansion of the capabilities of data processing systems. Engineering a CSP system requires the combination of human and machine computation elements. From a general systems theory perspective, this means taking into account inherited as well as emerging properties from both these elements. In this paper, we position CSP systems within a broader taxonomy, outline a series of design principles and evaluation metrics, present an extensible framework for their design, and describe several design patterns. We showcase the capabilities of CSP systems by performing a case study that applies our proposed framework to the design and analysis of a real system (AIDR) that classifies social media messages during time-critical crisis events. Results show that compared to a pure stream processing system, AIDR can achieve a higher data classification accuracy, while compared to a pure crowdsourcing solution, the system makes better use of human workers by requiring much less manual work effort

The 64 Mpixel wide field imager for the Wendelstein 2m Telescope: Design and Calibration

The Wendelstein Observatory of Ludwig Maximilians University of Munich has recently been upgraded with a modern 2m robotic telescope. One Nasmyth port of the telescope has been equipped with a wide-field corrector which preserves the excellent image quality (< 0.8" median seeing) of the site (Hopp et al. 2008) over a field of view of 0.7 degrees diameter. The available field is imaged by an optical imager (WWFI, the Wendelstein Wide Field Imager) built around a customized 2 $\times$ 2 mosaic of 4k $\times$ 4k 15 \mu m e2v CCDs from Spectral Instruments. This paper provides an overview of the design and the WWFI's performance. We summarize the system mechanics (including a structural analysis), the electronics (and its electromagnetic interference (EMI) protection) and the control software. We discuss in detail detector system parameters, i.e. gain and readout noise, quantum efficiency as well as charge transfer efficiency (CTE) and persistent charges. First on sky tests yield overall good predictability of system throughput based on lab measurements.Comment: 38 pages 19 Figures To be published in Springer Experimental Astronom

On the Interface Between Operations and Human Resources Management

Operations management (OM) and human resources management (HRM) have historically been very separate fields. In practice, operations managers and human resource managers interact primarily on administrative issues regarding payroll and other matters. In academia, the two subjects are studied by separate communities of scholars publishing in disjoint sets of journals, drawing on mostly separate disciplinary foundations. Yet, operations and human resources are intimately related at a fundamental level. Operations are the context that often explains or moderates the effects of human resource activities such as pay, training, communications and staffing. Human responses to operations management systems often explain variations or anomalies that would otherwise be treated as randomness or error variance in traditional operations research models. In this paper, we probe the interface between operations and human resources by examining how human considerations affect classical OM results and how operational considerations affect classical HRM results. We then propose a unifying framework for identifying new research opportunities at the intersection of the two fields

Pseudorandom number generation with self programmable cellular automata

In this paper, we propose a new class of cellular automata – self programming cellular automata (SPCA) with specific application to pseudorandom number generation. By changing a cell's state transition rules in relation to factors such as its neighboring cell's states, behavioral complexity can be increased and utilized. Interplay between the state transition neighborhood and rule selection neighborhood leads to a new composite neighborhood and state transition rule that is the linear combination of two different mappings with different temporal dependencies. It is proved that when the transitional matrices for both the state transition and rule selection neighborhood are non-singular, SPCA will not exhibit non-group behavior. Good performance can be obtained using simple neighborhoods with certain CA length, transition rules etc. Certain configurations of SPCA pass all DIEHARD and ENT tests with an implementation cost lower than current reported work. Output sampling methods are also suggested to improve output efficiency by sampling the outputs of the new rule selection neighborhoods