An energy‐aware performance analysis of SWIMM: Smith–Waterman implementation on Intel's Multicore and Manycore architectures

Alignment is essential in many areas such as biological, chemical and criminal forensics. The well‐known Smith–Waterman (SW) algorithm is able to retrieve the optimal local alignment with quadratic time and space complexity. There are several implementations that take advantage of computing parallelization, such as manycores, FPGAs or GPUs, in order to reduce the alignment effort. In this research, we adapt, develop and tune the SW algorithm named SWIMM on a heterogeneous platform based on Intel's Xeon and Xeon Phi coprocessor. SWIMM is a free tool available in a public git repository https://github.com/enzorucci/SWIMM. We efficiently exploit data and thread‐level parallelism, reaching up to 380 GCUPS on heterogeneous architecture, 350 GCUPS for the isolated Xeon and 50 GCUPS on Xeon Phi. Despite the heterogeneous implementation obtaining the best performance, it is also the most energy‐demanding. In fact, we also present a trade‐off analysis between performance and power consumption. The greenest configuration is based on an isolated multicore system that exploits AVX2 instruction set architecture reaching 1.5 GCUPS/Watts.Facultad de Informátic

Vector-Processing for Mobile Devices: Benchmark and Analysis

Vector processing has become commonplace in today's CPU microarchitectures. Vector instructions improve performance and energy which is crucial for resource-constraint mobile devices. The research community currently lacks a comprehensive benchmark suite to study the benefits of vector processing for mobile devices. This paper presents Swan-an extensive vector processing benchmark suite for mobile applications. Swan consists of a diverse set of data-parallel workloads from four commonly used mobile applications: operating system, web browser, audio/video messaging application, and PDF rendering engine. Using Swan benchmark suite, we conduct a detailed analysis of the performance, power, and energy consumption of vectorized workloads, and show that: (a) Vectorized kernels increase the pressure on cache hierarchy due to the higher rate of memory requests. (b) Vector processing is more beneficial for workloads with lower precision operations and higher cache hit rates. (c) Limited Instruction-Level Parallelism and strided memory accesses to multi-dimensional data structures prevent vector processing benefits from scaling with more SIMD functional units and wider registers. (d) Despite lower computation throughput than domain-specific accelerators, such as GPU, vector processing outperforms these accelerators for kernels with lower operation counts. Finally, we show five common computation patterns in mobile data-parallel workloads that dominate the execution time.Comment: 2023 IEEE International Symposium on Workload Characterization (IISWC

A new parallelisation technique for heterogeneous CPUs

Parallelization has moved in recent years into the mainstream compilers, and the demand for parallelizing tools that can do a better job of automatic parallelization is higher than ever. During the last decade considerable attention has been focused on developing programming tools that support both explicit and implicit parallelism to keep up with the power of the new multiple core technology. Yet the success to develop automatic parallelising compilers has been limited mainly due to the complexity of the analytic process required to exploit available parallelism and manage other parallelisation measures such as data partitioning, alignment and synchronization. This dissertation investigates developing a programming tool that automatically parallelises large data structures on a heterogeneous architecture and whether a high-level programming language compiler can use this tool to exploit implicit parallelism and make use of the performance potential of the modern multicore technology. The work involved the development of a fully automatic parallelisation tool, called VSM, that completely hides the underlying details of general purpose heterogeneous architectures. The VSM implementation provides direct and simple access for users to parallelise array operations on the Cell’s accelerators without the need for any annotations or process directives. This work also involved the extension of the Glasgow Vector Pascal compiler to work with the VSM implementation as a one compiler system. The developed compiler system, which is called VP-Cell, takes a single source code and parallelises array expressions automatically. Several experiments were conducted using Vector Pascal benchmarks to show the validity of the VSM approach. The VP-Cell system achieved significant runtime performance on one accelerator as compared to the master processor’s performance and near-linear speedups over code runs on the Cell’s accelerators. Though VSM was mainly designed for developing parallelising compilers it also showed a considerable performance by running C code over the Cell’s accelerators

Multi-Softcore Architecture on FPGA

To meet the high performance demands of embedded multimedia applications, embedded systems are integrating multiple processing units. However, they are mostly based on custom-logic design methodology. Designing parallel multicore systems using available standards intellectual properties yet maintaining high performance is also a challenging issue. Softcore processors and field programmable gate arrays (FPGAs) are a cheap and fast option to develop and test such systems. This paper describes a FPGA-based design methodology to implement a rapid prototype of parametric multicore systems. A study of the viability of making the SoC using the NIOS II soft-processor core from Altera is also presented. The NIOS II features a general-purpose RISC CPU architecture designed to address a wide range of applications. The performance of the implemented architecture is discussed, and also some parallel applications are used for testing speedup and efficiency of the system. Experimental results demonstrate the performance of the proposed multicore system, which achieves better speedup than the GPU (29.5% faster for the FIR filter and 23.6% faster for the matrix-matrix multiplication)

A vector-µSIMD-VLIW architecture for multimedia applications

Media processing has motivated strong changes in the focus and design of processors. These applications are composed of heterogeneous regions of code, some of them with high levels of DLP and other ones with only modest amounts of ILP. A common approach to deal with these applications are /spl mu/SIMD-VLIWprocessors. However, the ILP regions fail to scale when we increase the width of the machine, which, on the other hand, is desired to achieve high performance in the DLP regions. In this paper, we propose and evaluate adding vector capabilities to a /spl mu/SIMD-VLIW core to speed-up the execution of the DLP regions, while, at the same time, reducing the fetch bandwidth requirements. Results show that, in the DLP regions, both 2 and 4-issue width vector-/spl mu/SIMD-VLIW architectures outperform a 8-issue width /spl mu/SIMD-VLIW in factors of up to 2.7X and 4.2X (1.6X and 2.1X in average) respectively. As a result, the DLP regions become less than 10% of the total execution time and performance is dominated by the ILP regions.Peer ReviewedPostprint (published version

Precision-Energy-Throughput Scaling Of Generic Matrix Multiplication and Convolution Kernels Via Linear Projections

Generic matrix multiplication (GEMM) and one-dimensional convolution/cross-correlation (CONV) kernels often constitute the bulk of the compute- and memory-intensive processing within image/audio recognition and matching systems. We propose a novel method to scale the energy and processing throughput of GEMM and CONV kernels for such error-tolerant multimedia applications by adjusting the precision of computation. Our technique employs linear projections to the input matrix or signal data during the top-level GEMM and CONV blocking and reordering. The GEMM and CONV kernel processing then uses the projected inputs and the results are accumulated to form the final outputs. Throughput and energy scaling takes place by changing the number of projections computed by each kernel, which in turn produces approximate results, i.e. changes the precision of the performed computation. Results derived from a voltage- and frequency-scaled ARM Cortex A15 processor running face recognition and music matching algorithms demonstrate that the proposed approach allows for 280%~440% increase of processing throughput and 75%~80% decrease of energy consumption against optimized GEMM and CONV kernels without any impact in the obtained recognition or matching accuracy. Even higher gains can be obtained if one is willing to tolerate some reduction in the accuracy of the recognition and matching applications