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

Design of a High-Speed Architecture for Stabilization of Video Captured Under Non-Uniform Lighting Conditions

Video captured in shaky conditions may lead to vibrations. A robust algorithm to immobilize the video by compensating for the vibrations from physical settings of the camera is presented in this dissertation. A very high performance hardware architecture on Field Programmable Gate Array (FPGA) technology is also developed for the implementation of the stabilization system. Stabilization of video sequences captured under non-uniform lighting conditions begins with a nonlinear enhancement process. This improves the visibility of the scene captured from physical sensing devices which have limited dynamic range. This physical limitation causes the saturated region of the image to shadow out the rest of the scene. It is therefore desirable to bring back a more uniform scene which eliminates the shadows to a certain extent. Stabilization of video requires the estimation of global motion parameters. By obtaining reliable background motion, the video can be spatially transformed to the reference sequence thereby eliminating the unintended motion of the camera. A reflectance-illuminance model for video enhancement is used in this research work to improve the visibility and quality of the scene. With fast color space conversion, the computational complexity is reduced to a minimum. The basic video stabilization model is formulated and configured for hardware implementation. Such a model involves evaluation of reliable features for tracking, motion estimation, and affine transformation to map the display coordinates of a stabilized sequence. The multiplications, divisions and exponentiations are replaced by simple arithmetic and logic operations using improved log-domain computations in the hardware modules. On Xilinx\u27s Virtex II 2V8000-5 FPGA platform, the prototype system consumes 59% logic slices, 30% flip-flops, 34% lookup tables, 35% embedded RAMs and two ZBT frame buffers. The system is capable of rendering 180.9 million pixels per second (mpps) and consumes approximately 30.6 watts of power at 1.5 volts. With a 1024×1024 frame, the throughput is equivalent to 172 frames per second (fps). Future work will optimize the performance-resource trade-off to meet the specific needs of the applications. It further extends the model for extraction and tracking of moving objects as our model inherently encapsulates the attributes of spatial distortion and motion prediction to reduce complexity. With these parameters to narrow down the processing range, it is possible to achieve a minimum of 20 fps on desktop computers with Intel Core 2 Duo or Quad Core CPUs and 2GB DDR2 memory without a dedicated hardware

A novel algorithm and hardware architecture for fast video-based shape reconstruction of space debris

In order to enable the non-cooperative rendezvous, capture, and removal of large space debris, automatic recognition of the target is needed. Video-based techniques are the most suitable in the strict context of space missions, where low-energy consumption is fundamental, and sensors should be passive in order to avoid any possible damage to external objects as well as to the chaser satellite. This paper presents a novel fast shape-from-shading (SfS) algorithm and a field-programmable gate array (FPGA)-based system hardware architecture for video-based shape reconstruction of space debris. The FPGA-based architecture, equipped with a pair of cameras, includes a fast image pre-processing module, a core implementing a feature-based stereo-vision approach, and a processor that executes the novel SfS algorithm. Experimental results show the limited amount of logic resources needed to implement the proposed architecture, and the timing improvements with respect to other state-of-the-art SfS methods. The remaining resources available in the FPGA device can be exploited to integrate other vision-based techniques to improve the comprehension of debris model, allowing a fast evaluation of associated kinematics in order to select the most appropriate approach for capture of the target space debris

Dynamically reconfigurable architecture for embedded computer vision systems

The objective of this research work is to design, develop and implement a new architecture which integrates on the same chip all the processing levels of a complete Computer Vision system, so that the execution is efficient without compromising the power consumption while keeping a reduced cost. For this purpose, an analysis and classification of different mathematical operations and algorithms commonly used in Computer Vision are carried out, as well as a in-depth review of the image processing capabilities of current-generation hardware devices. This permits to determine the requirements and the key aspects for an efficient architecture. A representative set of algorithms is employed as benchmark to evaluate the proposed architecture, which is implemented on an FPGA-based system-on-chip. Finally, the prototype is compared to other related approaches in order to determine its advantages and weaknesses

LFRic: meeting the challenges of scalability and performance portability in weather and climate models

This paper describes LFRic: the new weather and climate modelling system being developed by the UK Met Office to replace the existing Unified Model in preparation for exascale computing in the 2020s. LFRic uses the GungHo dynamical core and runs on a semi-structured cubed-sphere mesh. The design of the supporting infrastructure follows object-oriented principles to facilitate modularity and the use of external libraries where possible. In particular, a `separation of concerns' between the science code and parallel code is imposed to promote performance portability. An application called PSyclone, developed at the STFC Hartree centre, can generate the parallel code enabling deployment of a single source science code onto different machine architectures. This paper provides an overview of the scientific requirement, the design of the software infrastructure, and examples of PSyclone usage. Preliminary performance results show strong scaling and an indication that hybrid MPI/OpenMP performs better than pure MPI

A Neural Signal Processor for Low-Latency Spike Inference

This thesis describes the development of a system that can assign identities to a population of single-units, in multi-electrode recordings, at single-spike resolution with low-latency. The system has two parts. The first is a Field-Programmable Gate Array (FPGA)-based Neural Signal Processor (NSP) that receives raw input and generates labelled spikes as output, a process referred to as real-time spike inference. The second is a piece of software (Spiketag) that runs on a PC, communicates with the NSP, and generates a spike-sorted model to guide the real-time spike inference. The NSP provides clocks and control signals to five 32-channel INTAN RHD2132 chips to manage the acquisition of 160 channels of raw neural data. In parallel, the NSP further filters, detects and extracts extracellular spike waveforms from the raw neural data recorded by tetrodes or silicon probes and assigns single-unit identity to each detected spike. A set of Python application programming interfaces (APIs) was developed in Spiketag to enable the communication between the NSP and the PC. These APIs allow the NSP to obtain a model from the PC, which holds parameters such as reference channels, spike detection thresholds, spike feature transformation matrix and vector quantized clusters generated by spike sorting a short recording session. Using the spike-sorted model, the NSP performs data acquisition and real-time spike inference simultaneously. Algorithmic modules were implemented in the FPGA and pipelined to compute during 40 ms acquisition intervals. At the output end of the FPGA NSP, the real-time assigned single-unit identity (spike-id) is packaged with the timestamp, the electrode group, and the spike features as a spike-id packet. Spike-id packets are asynchronously transmitted through a low-latency Peripheral Component Interconnect Express (PCIe) interface to the PC, producing the real-time spike trains. The real-time spike trains can be used for further processing, such as real-time decoding. Several types of ground-truth data, including intracellular/extracellular paired recordings, synthesized tetrode extracellular waveforms with ground-truth spike timing and high-channel-count silicon probe recordings with ground-truth animal positions during navigation were used to validate the low-latency (1 ms) and high-accuracy (as high as state-of-the-art offline sorting and decoding algorithms) of the NSP’s real-time spike inference and the NSP-based real-time population decoding performance

Kodizajn arhitekture i algoritama za lokalizacijumobilnih robota i detekciju prepreka baziranih namodelu

This thesis proposes SoPC (System on a Programmable Chip) architectures for efficient embedding of vison-based localization and obstacle detection tasks in a navigational pipeline on autonomous mobile robots. The obtained results are equivalent or better in comparison to state-ofthe- art. For localization, an efficient hardware architecture that supports EKF-SLAM's local map management with seven-dimensional landmarks in real time is developed. For obstacle detection a novel method of object recognition is proposed - detection by identification framework based on single detection window scale. This framework allows adequate algorithmic precision and execution speeds on embedded hardware platforms.Ova teza bavi se dizajnom SoPC (engl. System on a Programmable Chip) arhitektura i algoritama za efikasnu implementaciju zadataka lokalizacije i detekcije prepreka baziranih na viziji u kontekstu autonomne robotske navigacije. Za lokalizaciju, razvijena je efikasna računarska arhitektura za EKF-SLAM algoritam, koja podržava skladištenje i obradu sedmodimenzionalnih orijentira lokalne mape u realnom vremenu. Za detekciju prepreka je predložena nova metoda prepoznavanja objekata u slici putem prozora detekcije fiksne dimenzije, koja omogućava veću brzinu izvršavanja algoritma detekcije na namenskim računarskim platformama

Accelerated volumetric reconstruction from uncalibrated camera views

While both work with images, computer graphics and computer vision are inverse problems. Computer graphics starts traditionally with input geometric models and produces image sequences. Computer vision starts with input image sequences and produces geometric models. In the last few years, there has been a convergence of research to bridge the gap between the two fields. This convergence has produced a new field called Image-based Rendering and Modeling (IBMR). IBMR represents the effort of using the geometric information recovered from real images to generate new images with the hope that the synthesized ones appear photorealistic, as well as reducing the time spent on model creation. In this dissertation, the capturing, geometric and photometric aspects of an IBMR system are studied. A versatile framework was developed that enables the reconstruction of scenes from images acquired with a handheld digital camera. The proposed system targets applications in areas such as Computer Gaming and Virtual Reality, from a lowcost perspective. In the spirit of IBMR, the human operator is allowed to provide the high-level information, while underlying algorithms are used to perform low-level computational work. Conforming to the latest architecture trends, we propose a streaming voxel carving method, allowing a fast GPU-based processing on commodity hardware