BrainFrame: A node-level heterogeneous accelerator platform for neuron simulations

Objective: The advent of High-Performance Computing (HPC) in recent years has led to its increasing use in brain study through computational models. The scale and complexity of such models are constantly increasing, leading to challenging computational requirements. Even though modern HPC platforms can often deal with such challenges, the vast diversity of the modeling field does not permit for a single acceleration (or homogeneous) platform to effectively address the complete array of modeling requirements. Approach: In this paper we propose and build BrainFrame, a heterogeneous acceleration platform, incorporating three distinct acceleration technologies, a Dataflow Engine, a Xeon Phi and a GP-GPU. The PyNN framework is also integrated into the platform. As a challenging proof of concept, we analyze the performance of BrainFrame on different instances of a state-of-the-art neuron model, modeling the Inferior- Olivary Nucleus using a biophysically-meaningful, extended Hodgkin-Huxley representation. The model instances take into account not only the neuronal- network dimensions but also different network-connectivity circumstances that can drastically change application workload characteristics. Main results: The synthetic approach of three HPC technologies demonstrated that BrainFrame is better able to cope with the modeling diversity encountered. Our performance analysis shows clearly that the model directly affect performance and all three technologies are required to cope with all the model use cases.Comment: 16 pages, 18 figures, 5 table

Highly parallel computation

Highly parallel computing architectures are the only means to achieve the computation rates demanded by advanced scientific problems. A decade of research has demonstrated the feasibility of such machines and current research focuses on which architectures designated as multiple instruction multiple datastream (MIMD) and single instruction multiple datastream (SIMD) have produced the best results to date; neither shows a decisive advantage for most near-homogeneous scientific problems. For scientific problems with many dissimilar parts, more speculative architectures such as neural networks or data flow may be needed

Resource management for data streaming applications

This dissertation investigates novel middleware mechanisms for building streaming applications. Developing streaming applications is a challenging task because (i) they are continuous in nature; (ii) they require fusion of data coming from multiple sources to derive higher level information; (iii) they require efficient transport of data from/to distributed sources and sinks; (iv) they need access to heterogeneous resources spanning sensor networks and high performance computing; and (v) they are time critical in nature. My thesis is that an intuitive programming abstraction will make it easier to build dynamic, distributed, and ubiquitous data streaming applications. Moreover, such an abstraction will enable an efficient allocation of shared and heterogeneous computational resources thereby making it easier for domain experts to build these applications. In support of the thesis, I present a novel programming abstraction, called DFuse, that makes it easier to develop these applications. A domain expert only needs to specify the input and output connections to fusion channels, and the fusion functions. The subsystems developed in this dissertation take care of instantiating the application, allocating resources for the application (via the scheduling heuristic developed in this dissertation) and dynamically managing the resources (via the dynamic scheduling algorithm presented in this dissertation). Through extensive performance evaluation, I demonstrate that the resources are allocated efficiently to optimize the throughput and latency constraints of an application.Ph.D.Committee Chair: Ramachandran, Umakishore; Committee Member: Chervenak, Ann; Committee Member: Cooper, Brian; Committee Member: Liu, Ling; Committee Member: Schwan, Karste

A Networked Dataflow Simulation Environment for Signal Processing and Data Mining Applications

In networked signal processing systems, dataflow graphs can be used to describe the processing on individual network nodes. However, to analyze the correctness and performance of these systems, designers must understand the interactions across these individual "node-level'' dataflow graphs --- as they communicate across the network --- in addition to the characteristics of the individual graphs. In this thesis, we present a novel simulation environment, called the NS-2 -- TDIF SIMulation environment (NT-SIM). NT-SIM provides integrated co-simulation of networked systems and combines the network analysis capabilities provided by the Network Simulator (ns) with the scheduling capabilities of a dataflow-based framework, thereby providing novel features for more comprehensive simulation of networked signal processing systems. Through a novel integration of advanced tools for network and dataflow graph simulation, our NT-SIM environment allows comprehensive simulation and analysis of networked systems. We present two case studies that concretely demonstrate the utility of NT-SIM in the contexts of a heterogeneous signal processing and data mining system design

DALiuGE: A Graph Execution Framework for Harnessing the Astronomical Data Deluge

The Data Activated Liu Graph Engine - DALiuGE - is an execution framework for processing large astronomical datasets at a scale required by the Square Kilometre Array Phase 1 (SKA1). It includes an interface for expressing complex data reduction pipelines consisting of both data sets and algorithmic components and an implementation run-time to execute such pipelines on distributed resources. By mapping the logical view of a pipeline to its physical realisation, DALiuGE separates the concerns of multiple stakeholders, allowing them to collectively optimise large-scale data processing solutions in a coherent manner. The execution in DALiuGE is data-activated, where each individual data item autonomously triggers the processing on itself. Such decentralisation also makes the execution framework very scalable and flexible, supporting pipeline sizes ranging from less than ten tasks running on a laptop to tens of millions of concurrent tasks on the second fastest supercomputer in the world. DALiuGE has been used in production for reducing interferometry data sets from the Karl E. Jansky Very Large Array and the Mingantu Ultrawide Spectral Radioheliograph; and is being developed as the execution framework prototype for the Science Data Processor (SDP) consortium of the Square Kilometre Array (SKA) telescope. This paper presents a technical overview of DALiuGE and discusses case studies from the CHILES and MUSER projects that use DALiuGE to execute production pipelines. In a companion paper, we provide in-depth analysis of DALiuGE's scalability to very large numbers of tasks on two supercomputing facilities.Comment: 31 pages, 12 figures, currently under review by Astronomy and Computin

Pando: Personal Volunteer Computing in Browsers

The large penetration and continued growth in ownership of personal electronic devices represents a freely available and largely untapped source of computing power. To leverage those, we present Pando, a new volunteer computing tool based on a declarative concurrent programming model and implemented using JavaScript, WebRTC, and WebSockets. This tool enables a dynamically varying number of failure-prone personal devices contributed by volunteers to parallelize the application of a function on a stream of values, by using the devices' browsers. We show that Pando can provide throughput improvements compared to a single personal device, on a variety of compute-bound applications including animation rendering and image processing. We also show the flexibility of our approach by deploying Pando on personal devices connected over a local network, on Grid5000, a French-wide computing grid in a virtual private network, and seven PlanetLab nodes distributed in a wide area network over Europe.Comment: 14 pages, 12 figures, 2 table

Dynamic resource allocation in a hierarchical multiprocessor system: A preliminary study

An integrated system approach to dynamic resource allocation is proposed. Some of the problems in dynamic resource allocation and the relationship of these problems to system structures are examined. A general dynamic resource allocation scheme is presented. A hierarchial system architecture which dynamically maps between processor structure and programs at multiple levels of instantiations is described. Simulation experiments were conducted to study dynamic resource allocation on the proposed system. Preliminary evaluation based on simple dynamic resource allocation algorithms indicates that with the proposed system approach, the complexity of dynamic resource management could be significantly reduced while achieving reasonable effective dynamic resource allocation