Parallelization of dynamic programming recurrences in computational biology

The rapid growth of biosequence databases over the last decade has led to a performance bottleneck in the applications analyzing them. In particular, over the last five years DNA sequencing capacity of next-generation sequencers has been doubling every six months as costs have plummeted. The data produced by these sequencers is overwhelming traditional compute systems. We believe that in the future compute performance, not sequencing, will become the bottleneck in advancing genome science. In this work, we investigate novel computing platforms to accelerate dynamic programming algorithms, which are popular in bioinformatics workloads. We study algorithm-specific hardware architectures that exploit fine-grained parallelism in dynamic programming kernels using field-programmable gate arrays: FPGAs). We advocate a high-level synthesis approach, using the recurrence equation abstraction to represent dynamic programming and polyhedral analysis to exploit parallelism. We suggest a novel technique within the polyhedral model to optimize for throughput by pipelining independent computations on an array. This design technique improves on the state of the art, which builds latency-optimal arrays. We also suggest a method to dynamically switch between a family of designs using FPGA reconfiguration to achieve a significant performance boost. We have used polyhedral methods to parallelize the Nussinov RNA folding algorithm to build a family of accelerators that can trade resources for parallelism and are between 15-130x faster than a modern dual core CPU implementation. A Zuker RNA folding accelerator we built on a single workstation with four Xilinx Virtex 4 FPGAs outperforms 198 3 GHz Intel Core 2 Duo processors. Furthermore, our design running on a single FPGA is an order of magnitude faster than competing implementations on similar-generation FPGAs and graphics processors. Our work is a step toward the goal of automated synthesis of hardware accelerators for dynamic programming algorithms

Design Space Exploration and Resource Management of Multi/Many-Core Systems

The increasing demand of processing a higher number of applications and related data on computing platforms has resulted in reliance on multi-/many-core chips as they facilitate parallel processing. However, there is a desire for these platforms to be energy-efficient and reliable, and they need to perform secure computations for the interest of the whole community. This book provides perspectives on the aforementioned aspects from leading researchers in terms of state-of-the-art contributions and upcoming trends

mAPN: Modeling, Analysis, and Exploration of Algorithmic and Parallelism Adaptivity

Using parallel embedded systems these days is increasing. They are getting more complex due to integrating multiple functionalities in one application or running numerous ones concurrently. This concerns a wide range of applications, including streaming applications, commonly used in embedded systems. These applications must implement adaptable and reliable algorithms to deliver the required performance under varying circumstances (e.g., running applications on the platform, input data, platform variety, etc.). Given the complexity of streaming applications, target systems, and adaptivity requirements, designing such systems with traditional programming models is daunting. This is why model-based strategies with an appropriate Model of Computation (MoC) have long been studied for embedded system design. This work provides algorithmic adaptivity on top of parallelism for dynamic dataflow to express larger sets of variants. We present a multi-Alternative Process Network (mAPN), a high-level abstract representation in which several variants of the same application coexist in the same graph expressing different implementations. We introduce mAPN properties and its formalism to describe various local implementation alternatives. Furthermore, mAPNs are enriched with metadata to Provide the alternatives with quantitative annotations in terms of a specific metric. To help the user analyze the rich space of variants, we propose a methodology to extract feasible variants under user and hardware constraints. At the core of the methodology is an algorithm for computing global metrics of an execution of different alternatives from a compact mAPN specification. We validate our approach by exploring several possible variants created for the Automatic Subtitling Application (ASA) on two hardware platforms.Comment: 26 PAGES JOURNAL PAPE

Tangible user interfaces : past, present and future directions

In the last two decades, Tangible User Interfaces (TUIs) have emerged as a new interface type that interlinks the digital and physical worlds. Drawing upon users' knowledge and skills of interaction with the real non-digital world, TUIs show a potential to enhance the way in which people interact with and leverage digital information. However, TUI research is still in its infancy and extensive research is required in or- der to fully understand the implications of tangible user interfaces, to develop technologies that further bridge the digital and the physical, and to guide TUI design with empirical knowledge. This paper examines the existing body of work on Tangible User In- terfaces. We start by sketching the history of tangible user interfaces, examining the intellectual origins of this field. We then present TUIs in a broader context, survey application domains, and review frame- works and taxonomies. We also discuss conceptual foundations of TUIs including perspectives from cognitive sciences, phycology, and philoso- phy. Methods and technologies for designing, building, and evaluating TUIs are also addressed. Finally, we discuss the strengths and limita- tions of TUIs and chart directions for future research

Improving Model-Based Software Synthesis: A Focus on Mathematical Structures

Computer hardware keeps increasing in complexity. Software design needs to keep up with this. The right models and abstractions empower developers to leverage the novelties of modern hardware. This thesis deals primarily with Models of Computation, as a basis for software design, in a family of methods called software synthesis. We focus on Kahn Process Networks and dataflow applications as abstractions, both for programming and for deriving an efficient execution on heterogeneous multicores. The latter we accomplish by exploring the design space of possible mappings of computation and data to hardware resources. Mapping algorithms are not at the center of this thesis, however. Instead, we examine the mathematical structure of the mapping space, leveraging its inherent symmetries or geometric properties to improve mapping methods in general. This thesis thoroughly explores the process of model-based design, aiming to go beyond the more established software synthesis on dataflow applications. We starting with the problem of assessing these methods through benchmarking, and go on to formally examine the general goals of benchmarks. In this context, we also consider the role modern machine learning methods play in benchmarking. We explore different established semantics, stretching the limits of Kahn Process Networks. We also discuss novel models, like Reactors, which are designed to be a deterministic, adaptive model with time as a first-class citizen. By investigating abstractions and transformations in the Ohua language for implicit dataflow programming, we also focus on programmability. The focus of the thesis is in the models and methods, but we evaluate them in diverse use-cases, generally centered around Cyber-Physical Systems. These include the 5G telecommunication standard, automotive and signal processing domains. We even go beyond embedded systems and discuss use-cases in GPU programming and microservice-based architectures

Proceedings of the first international workshop on Investigating dataflow in embedded computing architectures (IDEA 2015), January 21, 2015, Amsterdam, The Netherlands

IDEA '15 held at HiPEAC 2015, Amsterdam, The Netherlands on January 21st, 2015 is the rst workshop on Investigating Data ow in Embedded computing Architectures. This technical report comprises of the proceedings of IDEA '15. Over the years, data ow has been gaining popularity among Embedded Systems researchers around Europe and the world. However, research on data ow is limited to small pockets in dierent communities without a common forum for discussion. The goal of the workshop was to provide a platform to researchers and practitioners to present work on modelling and analysis of present and future high performance embedded computing architectures using data ow. Despite being the rst edition of the workshop, it was very pleasant to see a total of 14 submissions, out of which 6 papers were selected following a thorough reviewing process. All the papers were reviewed by at least 5 reviewers. This workshop could not have become a reality without the help of a Technical Program Committee (TPC). The TPC members not only did the hard work to give helpful reviews in time, but also participated in extensive discussion following the reviewing process, leading to an excellent workshop program and very valuable feedback to authors. Likewise, the Organisation Committee also deserves acknowledgment to make this workshop a successful event. We take this opportunity to thank everyone who contributed in making this workshop a success

Proceedings of the first international workshop on Investigating dataflow in embedded computing architectures (IDEA 2015), January 21, 2015, Amsterdam, The Netherlands

IDEA '15 held at HiPEAC 2015, Amsterdam, The Netherlands on January 21st, 2015 is the rst workshop on Investigating Data ow in Embedded computing Architectures. This technical report comprises of the proceedings of IDEA '15. Over the years, data ow has been gaining popularity among Embedded Systems researchers around Europe and the world. However, research on data ow is limited to small pockets in dierent communities without a common forum for discussion. The goal of the workshop was to provide a platform to researchers and practitioners to present work on modelling and analysis of present and future high performance embedded computing architectures using data ow. Despite being the rst edition of the workshop, it was very pleasant to see a total of 14 submissions, out of which 6 papers were selected following a thorough reviewing process. All the papers were reviewed by at least 5 reviewers. This workshop could not have become a reality without the help of a Technical Program Committee (TPC). The TPC members not only did the hard work to give helpful reviews in time, but also participated in extensive discussion following the reviewing process, leading to an excellent workshop program and very valuable feedback to authors. Likewise, the Organisation Committee also deserves acknowledgment to make this workshop a successful event. We take this opportunity to thank everyone who contributed in making this workshop a success