Runtime Scheduling, Allocation, and Execution of Real-Time Hardware Tasks onto Xilinx FPGAs Subject to Fault Occurrence

This paper describes a novel way to exploit the computation capabilities delivered by modern Field-Programmable Gate Arrays (FPGAs), not only towards a higher performance, but also towards an improved reliability. Computation-specific pieces of circuitry are dynamically scheduled and allocated to different resources on the chip based on a set of novel algorithms which are described in detail in this article. These algorithms consider most of the technological constraints existing in modern partially reconfigurable FPGAs as well as spontaneously occurring faults and emerging permanent damage in the silicon substrate of the chip. In addition, the algorithms target other important aspects such as communications and synchronization among the different computations that are carried out, either concurrently or at different times. The effectiveness of the proposed algorithms is tested by means of a wide range of synthetic simulations, and, notably, a proof-of-concept implementation of them using real FPGA hardware is outlined

High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs), Graphics Processor Units (GPUs), and IBM’s Cell Broadband Engine (Cell BE), in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion and perform better than all other platforms on performance per dollar criterion, although by a much smaller margin. Cell BE and GPU come second and third, respectively, on both performance per watt and performance per dollar criteria. In general, in order to outperform other technologies on performance per dollar criterion (using currently available hardware and development tools), FPGAs need to achieve at least two orders of magnitude speed-up compared to general-purpose processors and one order of magnitude speed-up compared to domain-specific technologies such as GPUs

Design and Evaluation of a BLAST Ungapped Extension Accelerator, Master\u27s Thesis

The amount of biosequence data being produced each year is growing exponentially. Extracting useful information from this massive amount of data is becoming an increasingly difficult task. This thesis focuses on accelerating the most widely-used software tool for analyzing genomic data, BLAST. This thesis presents Mercury BLAST, a novel method for accelerating searches through massive DNA databases. Mercury BLAST takes a streaming approach to the BLAST computation by offloading the performance-critical sections onto reconfigurable hardware. This hardware is then used in combination with the processor of the host system to deliver BLAST results in a fraction of the time of the general-purpose processor alone. Mercury BLAST makes use of new algorithms combined with reconfigurable hardware to accelerate BLAST-like similarity search. An evaluation of this method for use in real BLAST-like searches is presented along with a characterization of the quality of results associated with using these new algorithms in specialized hardware. The primary focus of this thesis is the design of the ungapped extension stage of Mercury BLAST. The architecture of the ungapped extension stage is described along with the context of this stage within the Mercury BLAST system. The design is compact and performs over 20× faster than that of the standard software ungapped extension, yielding close to 50× speedup over the complete software BLAST application. The quality of Mercury BLAST results is essentially equivalent to the standard BLAST results

Significant papers from the First 25 Years of the FPL Conference

The list of significant papers from the first 25 years of the Field-Programmable Logic and Applications conference (FPL) is presented in this paper. These 27 papers represent those which have most strongly influenced theory and practice in the field.postprin

Dataflow acceleration of Smith-Waterman with Traceback for high throughput Next Generation Sequencing

Smith-Waterman algorithm is widely adopted bymost popular DNA sequence aligners. The inherent algorithmcomputational intensity and the vast amount of NGS input datait operates on, create a bottleneck in genomic analysis flows forshort-read alignment. FPGA architectures have been extensivelyleveraged to alleviate the problem, each one adopting a differentapproach. In existing solutions, effective co-design of the NGSshort-read alignment still remains an open issue, mainly due tonarrow view on real integration aspects, such as system widecommunication and accelerator call overheads. In this paper, wepropose a dataflow architecture for Smith-Waterman Matrix-filland Traceback alignment stages, to perform short-read alignmenton NGS data. The architectural decision of moving both stages onchip extinguishes the communication overhead, and coupled withradical software restructuring, allows for efficient integration intowidely-used Bowtie2 aligner. This approach delivers×18 speedupover the respective Bowtie2 standalone components, while our co-designed Bowtie2 demonstrates a 35% boost in performance

A Survey of Processing Systems for Phylogenetics and Population Genetics

The COVID-19 pandemic brought Bioinformatics into the spotlight, revealing that several existing methods, algorithms, and tools were not well prepared to handle large amounts of genomic data efficiently. This led to prohibitively long execution times and the need to reduce the extent of analyses to obtain results in a reasonable amount of time. In this survey, we review available high-performance computing and hardware-accelerated systems based on FPGA and GPU technology. Optimized and hardware-accelerated systems can conduct more thorough analyses considerably faster than pure software implementations, allowing to reach important conclusions in a timely manner to drive scientific discoveries. We discuss the reasons that are currently hindering high-performance solutions from being widely deployed in real-world biological analyses and describe a research direction that can pave the way to enable this

10281 Abstracts Collection -- Dynamically Reconfigurable Architectures

From 11.07.10 to 16.07.10, Dagstuhl Seminar 10281 ``Dynamically Reconfigurable Architectures \u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

FPGA based remote code integrity verification of programs in distributed embedded systems

The explosive growth of networked embedded systems has made ubiquitous and pervasive computing a reality. However, there are still a number of new challenges to its widespread adoption that include scalability, availability, and, especially, security of software. Among the different challenges in software security, the problem of remote-code integrity verification is still waiting for efficient solutions. This paper proposes the use of reconfigurable computing to build a consistent architecture for generation of attestations (proofs) of code integrity for an executing program as well as to deliver them to the designated verification entity. Remote dynamic update of reconfigurable devices is also exploited to increase the complexity of mounting attacks in a real-word environment. The proposed solution perfectly fits embedded devices that are nowadays commonly equipped with reconfigurable hardware components that are exploited to solve different computational problems

Towards adaptive balanced computing (ABC) using reconfigurable functional caches (RFCs)

The general-purpose computing processor performs a wide range of functions. Although the performance of general-purpose processors has been steadily increasing, certain software technologies like multimedia and digital signal processing applications demand ever more computing power. Reconfigurable computing has emerged to combine the versatility of general-purpose processors with the customization ability of ASICs. The basic premise of reconfigurability is to provide better performance and higher computing density than fixed configuration processors. Most of the research in reconfigurable computing is dedicated to on-chip functional logic. If computing resources are adaptable to the computing requirement, the maximum performance can be achieved. To overcome the gap between processor and memory technology, the size of on-chip cache memory has been consistently increasing. The larger cache memory capacity, though beneficial in general, does not guarantee a higher performance for all the applications as they may not utilize all of the cache efficiently. To utilize on-chip resources effectively and to accelerate the performance of multimedia applications specifically, we propose a new architecture---Adaptive Balanced Computing (ABC). ABC uses dynamic resource configuration of on-chip cache memory by integrating Reconfigurable Functional Caches (RFC). RFC can work as a conventional cache or as a specialized computing unit when necessary. In order to convert a cache memory to a computing unit, we include additional logic to embed multi-bit output LUTs into the cache structure. We add the reconfigurability of cache memory to a conventional processor with minimal modification to the load/store microarchitecture and with minimal compiler assistance. ABC architecture utilizes resources more efficiently by reconfiguring the cache memory to computing units dynamically. The area penalty for this reconfiguration is about 50--60% of the memory cell cache array-only area with faster cache access time. In a base array cache (parallel decoding caches), the area penalty is 10--20% of the data array with 1--2% increase in the cache access time. However, we save 27% for FIR and 44% for DCT/IDCT in area with respect to memory cell array cache and about 80% for both applications with respect to base array cache if we were to implement all these units separately (such as ASICs). The simulations with multimedia and DSP applications (DCT/IDCT and FIR/IIR) show that the resource configuration with the RFC speedups ranging from 1.04X to 3.94X in overall applications and from 2.61X to 27.4X in the core computations. The simulations with various parameters indicate that the impact of reconfiguration can be minimized if an appropriate cache organization is selected