DeSyRe: on-Demand System Reliability

The DeSyRe project builds on-demand adaptive and reliable Systems-on-Chips (SoCs). As fabrication technology scales down, chips are becoming less reliable, thereby incurring increased power and performance costs for fault tolerance. To make matters worse, power density is becoming a significant limiting factor in SoC design, in general. In the face of such changes in the technological landscape, current solutions for fault tolerance are expected to introduce excessive overheads in future systems. Moreover, attempting to design and manufacture a totally defect and fault-free system, would impact heavily, even prohibitively, the design, manufacturing, and testing costs, as well as the system performance and power consumption. In this context, DeSyRe delivers a new generation of systems that are reliable by design at well-balanced power, performance, and design costs. In our attempt to reduce the overheads of fault-tolerance, only a small fraction of the chip is built to be fault-free. This fault-free part is then employed to manage the remaining fault-prone resources of the SoC. The DeSyRe framework is applied to two medical systems with high safety requirements (measured using the IEC 61508 functional safety standard) and tight power and performance constraints

Hardware co-processor to enable MIMO in next generation wireless networks

One prevailing technology in wireless communication is Multiple Input, Multiple Output (MIMO) communication. MIMO communication simultaneously transmits several data streams, each from their own antenna within the same frequency channel. This technique can increase data bandwidth by up to a factor of the number of transmitting antennas, but comes with the cost of a much higher computational complexity for the wireless receiver. MIMO communication exploits differing channel effects caused by physical distances between antennas to differentiate between transmitting antennas, an intrinsically two dimensional operation. Current Digital Signal Processors (DSPs), on the other hand, are designed to perform computations on one dimensional vectors of incoming data. To compensate for the lack of native support of these higher dimensional operations, current base stations are forced to add multiple new processing elements while many mobile devices cannot support MIMO communication. In order to allow wireless clients and stations to have native support of the two dimensional operations required by MIMO communication, a hardware co-processor was designed to allow the DSP to offload these operations onto another processor to reduce computation time

Combined flow cytometry and high-throughput image analysis for the study of essential genes in Caenorhabditis elegans

Background: Advances in automated image-based microscopy platforms coupled with high-throughput liquid workflows have facilitated the design of large-scale screens utilising multicellular model organisms such as Caenorhabditis elegans to identify genetic interactions, therapeutic drugs or disease modifiers. However, the analysis of essential genes has lagged behind because lethal or sterile mutations pose a bottleneck for high-throughput approaches, and a systematic way to analyse genetic interactions of essential genes in multicellular organisms has been lacking. Results: In C. elegans, non-conditional lethal mutations can be maintained in heterozygosity using chromosome balancers, commonly expressing green fluorescent protein (GFP) in the pharynx. However, gene expression or function is typically monitored by the use of fluorescent reporters marked with the same fluorophore, presenting a challenge to sort worm populations of interest, particularly at early larval stages. Here, we develop a sorting strategy capable of selecting homozygous mutants carrying a GFP stress reporter from GFP-balanced animals at the second larval stage. Because sorting is not completely error-free, we develop an automated high-throughput image analysis protocol that identifies and discards animals carrying the chromosome balancer. We demonstrate the experimental usefulness of combining sorting of homozygous lethal mutants and automated image analysis in a functional genomic RNA interference (RNAi) screen for genes that genetically interact with mitochondrial prohibitin (PHB). Lack of PHB results in embryonic lethality, while homozygous PHB deletion mutants develop into sterile adults due to maternal contribution and strongly induce the mitochondrial unfolded protein response (UPR mt ). In a chromosome-wide RNAi screen for C. elegans genes having human orthologues, we uncover both known and new PHB genetic interactors affecting the UPR mt and growth. Conclusions: The method presented here allows the study of balanced lethal mutations in a high-throughput manner. It can be easily adapted depending on the user's requirements and should serve as a useful resource for the C. elegans community for probing new biological aspects of essential nematode genes as well as the generation of more comprehensive genetic networks.European Research Council ERC-2011-StG-281691Ministerio de Economía y Competitividad BFU2012–3550

Trace-based Performance Analysis for Hardware Accelerators

This thesis presents how performance data from hardware accelerators can be included in event logs. It extends the capabilities of trace-based performance analysis to also monitor and record data from this novel parallelization layer. The increasing awareness to power consumption of computing devices has led to an interest in hybrid computing architectures as well. High-end computers, workstations, and mobile devices start to employ hardware accelerators to offload computationally intense and parallel tasks, while at the same time retaining a highly efficient scalar compute unit for non-parallel tasks. This execution pattern is typically asynchronous so that the scalar unit can resume other work while the hardware accelerator is busy. Performance analysis tools provided by the hardware accelerator vendors cover the situation of one host using one device very well. Yet, they do not address the needs of the high performance computing community. This thesis investigates ways to extend existing methods for recording events from highly parallel applications to also cover scenarios in which hardware accelerators aid these applications. After introducing a generic approach that is suitable for any API based acceleration paradigm, the thesis derives a suggestion for a generic performance API for hardware accelerators and its implementation with NVIDIA CUPTI. In a next step the visualization of event logs containing data from execution streams on different levels of parallelism is discussed. In order to overcome the limitations of classic performance profiles and timeline displays, a graph-based visualization using Parallel Performance Flow Graphs (PPFGs) is introduced. This novel technical approach is using program states in order to display similarities and differences between the potentially very large number of event streams and, thus, enables a fast way to spot load imbalances. The thesis concludes with the in-depth analysis of a case-study of PIConGPU---a highly parallel, multi-hybrid plasma physics simulation---that benefited greatly from the developed performance analysis methods.Diese Dissertation zeigt, wie der Ablauf von Anwendungsteilen, die auf Hardwarebeschleuniger ausgelagert wurden, als Programmspur mit aufgezeichnet werden kann. Damit wird die bekannte Technik der Leistungsanalyse von Anwendungen mittels Programmspuren so erweitert, dass auch diese neue Parallelitätsebene mit erfasst wird. Die Beschränkungen von Computersystemen bezüglich der elektrischen Leistungsaufnahme hat zu einer steigenden Anzahl von hybriden Computerarchitekturen geführt. Sowohl Hochleistungsrechner, aber auch Arbeitsplatzcomputer und mobile Endgeräte nutzen heute Hardwarebeschleuniger um rechenintensive, parallele Programmteile auszulagern und so den skalaren Hauptprozessor zu entlasten und nur für nicht parallele Programmteile zu verwenden. Dieses Ausführungsschema ist typischerweise asynchron: der Skalarprozessor kann, während der Hardwarebeschleuniger rechnet, selbst weiterarbeiten. Die Leistungsanalyse-Werkzeuge der Hersteller von Hardwarebeschleunigern decken den Standardfall (ein Host-System mit einem Hardwarebeschleuniger) sehr gut ab, scheitern aber an einer Unterstützung von hochparallelen Rechnersystemen. Die vorliegende Dissertation untersucht, in wie weit auch multi-hybride Anwendungen die Aktivität von Hardwarebeschleunigern aufzeichnen können. Dazu wird die vorhandene Methode zur Erzeugung von Programmspuren für hochparallele Anwendungen entsprechend erweitert. In dieser Untersuchung wird zuerst eine allgemeine Methodik entwickelt, mit der sich für jede API-gestützte Hardwarebeschleunigung eine Programmspur erstellen lässt. Darauf aufbauend wird eine eigene Programmierschnittstelle entwickelt, die es ermöglicht weitere leistungsrelevante Daten aufzuzeichnen. Die Umsetzung dieser Schnittstelle wird am Beispiel von NVIDIA CUPTI darstellt. Ein weiterer Teil der Arbeit beschäftigt sich mit der Darstellung von Programmspuren, welche Aufzeichnungen von den unterschiedlichen Parallelitätsebenen enthalten. Um die Einschränkungen klassischer Leistungsprofile oder Zeitachsendarstellungen zu überwinden, wird mit den parallelen Programmablaufgraphen (PPFGs) eine neue graphenbasisierte Darstellungsform eingeführt. Dieser neuartige Ansatz zeigt eine Programmspur als eine Folge von Programmzuständen mit gemeinsamen und unterchiedlichen Abläufen. So können divergierendes Programmverhalten und Lastimbalancen deutlich einfacher lokalisiert werden. Die Arbeit schließt mit der detaillierten Analyse von PIConGPU -- einer multi-hybriden Simulation aus der Plasmaphysik --, die in großem Maße von den in dieser Arbeit entwickelten Analysemöglichkeiten profiert hat

Profile-directed specialisation of custom floating-point hardware

We present a methodology for generating floating-point arithmetic hardware designs which are, for suitable applications, much reduced in size, while still retaining performance and IEEE-754 compliance. Our system uses three key parts: a profiling tool, a set of customisable floating-point units and a selection of system integration methods. We use a profiling tool for floating-point behaviour to identify arithmetic operations where fundamental elements of IEEE-754 floating-point may be compromised, without generating erroneous results in the common case. In the uncommon case, we use simple detection logic to determine when operands lie outside the range of capabilities of the optimised hardware. Out-of-range operations are handled by a separate, fully capable, floatingpoint implementation, either on-chip or by returning calculations to a host processor. We present methods of system integration to achieve this errorcorrection. Thus the system suffers no compromise in IEEE-754 compliance, even when the synthesised hardware would generate erroneous results. In particular, we identify from input operands the shift amounts required for input operand alignment and post-operation normalisation. For operations where these are small, we synthesise hardware with reduced-size barrel-shifters. We also propose optimisations to take advantage of other profile-exposed behaviours, including removing the hardware required to swap operands in a floating-point adder or subtractor, and reducing the exponent range to fit observed values. We present profiling results for a range of applications, including a selection of computational science programs, Spec FP 95 benchmarks and the FFMPEG media processing tool, indicating which would be amenable to our method. Selected applications which demonstrate potential for optimisation are then taken through to a hardware implementation. We show up to a 45% decrease in hardware size for a floating-point datapath, with a correctable error-rate of less then 3%, even with non-profiled datasets

Effective memory management for mobile environments

Smartphones, tablets, and other mobile devices exhibit vastly different constraints compared to regular or classic computing environments like desktops, laptops, or servers. Mobile devices run dozens of so-called “apps” hosted by independent virtual machines (VM). All these VMs run concurrently and each VM deploys purely local heuristics to organize resources like memory, performance, and power. Such a design causes conflicts across all layers of the software stack, calling for the evaluation of VMs and the optimization techniques specific for mobile frameworks. In this dissertation, we study the design of managed runtime systems for mobile platforms. More specifically, we deepen the understanding of interactions between garbage collection (GC) and system layers. We develop tools to monitor the memory behavior of Android-based apps and to characterize GC performance, leading to the development of new techniques for memory management that address energy constraints, time performance, and responsiveness. We implement a GC-aware frequency scaling governor for Android devices. We also explore the tradeoffs of power and performance in vivo for a range of realistic GC variants, with established benchmarks and real applications running on Android virtual machines. We control for variation due to dynamic voltage and frequency scaling (DVFS), Just-in-time (JIT) compilation, and across established dimensions of heap memory size and concurrency. Finally, we provision GC as a global service that collects statistics from all running VMs and then makes an informed decision that optimizes across all them (and not just locally), and across all layers of the stack. Our evaluation illustrates the power of such a central coordination service and garbage collection mechanism in improving memory utilization, throughput, and adaptability to user activities. In fact, our techniques aim at a sweet spot, where total on-chip energy is reduced (20–30%) with minimal impact on throughput and responsiveness (5–10%). The simplicity and efficacy of our approach reaches well beyond the usual optimization techniques

Low-Impact Profiling of Streaming, Heterogeneous Applications

Computer engineers are continually faced with the task of translating improvements in fabrication process technology: i.e., Moore\u27s Law) into architectures that allow computer scientists to accelerate application performance. As feature-size continues to shrink, architects of commodity processors are designing increasingly more cores on a chip. While additional cores can operate independently with some tasks: e.g. the OS and user tasks), many applications see little to no improvement from adding more processor cores alone. For many applications, heterogeneous systems offer a path toward higher performance. Significant performance and power gains have been realized by combining specialized processors: e.g., Field-Programmable Gate Arrays, Graphics Processing Units) with general purpose multi-core processors. Heterogeneous applications need to be programmed differently than traditional software. One approach, stream processing, fits these systems particularly well because of the segmented memories and explicit expression of parallelism. Unfortunately, debugging and performance tools that support streaming, heterogeneous applications do not exist. This dissertation presents TimeTrial, a performance measurement system that enables performance optimization of streaming applications by profiling the application deployed on a heterogeneous system. TimeTrial performs low-impact measurements by dedicating computing resources to monitoring and by aggressively compressing performance traces into statistical summaries guided by user specification of the performance queries of interest

PRODUCTIVELY SCALING HARDWARE DESIGNS OVER INCREASING RESOURCES USING A SYSTEMATIC DESIGN ANALYSIS APPROACH

As processor development shifts from strict single core frequency scaling to het- erogeneous resource scaling two important considerations require evaluation. First, how to design systems with an increasing amount of heterogeneous resources, and second, how to maintain a designer’s productivity as the number of possible con- figurations grows. Therefore, it is necessary to determine what useful information can be gathered from existing designs to help predict or identify a design’s potential scalability, as well as, identifying which routine tasks can be automated to improve a designer’s productivity. Moreover, once this information is collected, how can this information be conveyed to the designer such that it can be used to increase overall productivity when implementing the design over increasing amounts of resources? This research looks at various approaches to analyze designs and attempts to distribute an application efficiently across a heterogeneous cluster of computing re- sources through the use of a Systematic Design Analysis flow and an assortment of productivity tools. These tools provide the designer with projections on the amount of resources needed to scale an existing design to a specified performance, as well as, projecting the performance based on a specified amount of resources. This is accomplished through the combination of static HDL profiling, component synthesis resource utilization, and runtime performance monitoring. For evaluation, four case studies are presented to demonstrate the proposed flow’s scalability on a small scale cluster of FPGAs. The results are highly favorable, providing orders of magnitude speedup with minimal intervention from the designer