Peptide mass fingerprinting using field-programmable gate arrays

The reconfigurable computing paradigm, which exploits the flexibility and versatility of field-programmable gate arrays (FPGAs), has emerged as a powerful solution for speeding up time-critical algorithms. This paper describes a reconfigurable computing solution for processing raw mass spectrometric data generated by MALDI-TOF instruments. The hardware-implemented algorithms for denoising, baseline correction, peak identification, and deisotoping, running on a Xilinx Virtex-2 FPGA at 180 MHz, generate a mass fingerprint that is over 100 times faster than an equivalent algorithm written in C, running on a Dual 3-GHz Xeon server. The results obtained using the FPGA implementation are virtually identical to those generated by a commercial software package MassLynx

Mapping and Scheduling of Directed Acyclic Graphs on An FPFA Tile

An architecture for a hand-held multimedia device requires components that are energy-efficient, flexible, and provide high performance. In the CHAMELEON [4] project we develop a coarse grained reconfigurable device for DSP-like algorithms, the so-called Field Programmable Function Array (FPFA). The FPFA devices are reminiscent to FPGAs, but with a matrix of Processing Parts (PP) instead of CLBs. The design of the FPFA focuses on: (1) Keeping each PP small to maximize the number of PPs that can fit on a chip; (2) providing sufficient flexibility; (3) Low energy consumption; (4) Exploiting the maximum amount of parallelism; (5) A strong support tool for FPFA-based applications. The challenge in providing compiler support for the FPFA-based design stems from the flexibility of the FPFA structure. If we do not use the characteristics of the FPFA structure properly, the advantages of an FPFA may become its disadvantages. The GECKO1project focuses on this problem. In this paper, we present a mapping and scheduling scheme for applications running on one FPFA tile. Applications are written in C and C code is translated to a Directed Acyclic Graphs (DAG) [4]. This scheme can map a DAG directly onto the reconfigurable PPs of an FPFA tile. It tries to achieve low power consumption by exploiting locality of reference and high performance by exploiting maximum parallelism

Smart technologies for effective reconfiguration: the FASTER approach

Current and future computing systems increasingly require that their functionality stays flexible after the system is operational, in order to cope with changing user requirements and improvements in system features, i.e. changing protocols and data-coding standards, evolving demands for support of different user applications, and newly emerging applications in communication, computing and consumer electronics. Therefore, extending the functionality and the lifetime of products requires the addition of new functionality to track and satisfy the customers needs and market and technology trends. Many contemporary products along with the software part incorporate hardware accelerators for reasons of performance and power efficiency. While adaptivity of software is straightforward, adaptation of the hardware to changing requirements constitutes a challenging problem requiring delicate solutions. The FASTER (Facilitating Analysis and Synthesis Technologies for Effective Reconfiguration) project aims at introducing a complete methodology to allow designers to easily implement a system specification on a platform which includes a general purpose processor combined with multiple accelerators running on an FPGA, taking as input a high-level description and fully exploiting, both at design time and at run time, the capabilities of partial dynamic reconfiguration. The goal is that for selected application domains, the FASTER toolchain will be able to reduce the design and verification time of complex reconfigurable systems providing additional novel verification features that are not available in existing tool flows

Architecture for Document Clustering in Reconfigurable Hardware, Master\u27s Thesis, December 2006

High-performance document clustering systems enable similar documents to automatically self-organize into groups. In the past, the large amount of computational time needed to cluster documents prevented practical use of such systems with a large number of documents. A full hardware implementation of K-means clustering has been designed and implemented in reconfigurable hardware that rapidly clusters a half million documents. Documents and concepts are represented as vectors with 4000 dimensions. The circuit was implemented in Field Programmable Gate Array (FPGA) logic and uses four parallel cosine distance metrics to cluster document vectors together. An exploration of the effect of the integer approximation of the cosine theta distance metric was investigated. Through experiments, measurements were performed to determine the effect of utilizing different numeric representations for the concept vectors. As compared to a full K-means implementation in software, it was found that using carefully chosen integer representations yielded clustering results that were nearly identical to results obtained using full foating-point representations. Hardware was synthesized and run on the Field Programmable Port Extender (FPX) platform. This implementation on the Virtex-E 2000 FPGA ran 26 times faster than an algorithmically equivalent software running on an Intel 3.60 GHz Xeon. The same architecture was scaled to implement a faster and larger design for the Xilinx-4 LX200. This larger implementation outperformed the equivalent software version on the same Xeon by a factor of 328

Implementation of the K-Means Algorithm on Heterogeneous Devices: A Use Case Based on an Industrial Dataset

This paper presents and analyzes a heterogeneous implementation of an industrial use case based on K-means that targets symmetric multiprocessing (SMP), GPUs and FPGAs. We present how the application can be optimized from an algorithmic point of view and how this optimization performs on two heterogeneous platforms. The presented implementation relies on the OmpSs programming model, which introduces a simplified pragma-based syntax for the communication between the main processor and the accelerators. Performance improvement can be achieved by the programmer explicitly specifying the data memory accesses or copies. As expected, the newer SMP+GPU system studied is more powerful than the older SMP+FPGA system. However the latter is enough to fulfill the requirements of our use case and we show that uses less energy when considering only the active power of the execution.This work is partially supported by the European Union H2020 project AXIOM (grant agreement n. 645496), HiPEAC (grant agreement n. 687698), and Mont-Blanc (grant agreements n. 288777, 610402 and 671697), the Spanish Government Programa Severo Ochoa (SEV-2015-0493), the Spanish Ministry of Science and Technology (TIN2015- 65316-P) and the Departament d’Innovació, Universitats i Empresa de la Generalitat de Catalunya, under project MPEXPAR: Models de Programaci´o i Entorns d’Execució Paral·lels (2014-SGR-1051).Peer ReviewedPostprint (author's final draft

A committee machine gas identification system based on dynamically reconfigurable FPGA

This paper proposes a gas identification system based on the committee machine (CM) classifier, which combines various gas identification algorithms, to obtain a unified decision with improved accuracy. The CM combines five different classifiers: K nearest neighbors (KNNs), multilayer perceptron (MLP), radial basis function (RBF), Gaussian mixture model (GMM), and probabilistic principal component analysis (PPCA). Experiments on real sensors' data proved the effectiveness of our system with an improved accuracy over individual classifiers. Due to the computationally intensive nature of CM, its implementation requires significant hardware resources. In order to overcome this problem, we propose a novel time multiplexing hardware implementation using a dynamically reconfigurable field programmable gate array (FPGA) platform. The processing is divided into three stages: sampling and preprocessing, pattern recognition, and decision stage. Dynamically reconfigurable FPGA technique is used to implement the system in a sequential manner, thus using limited hardware resources of the FPGA chip. The system is successfully tested for combustible gas identification application using our in-house tin-oxide gas sensors