Copernicus: Characterizing the Performance Implications of Compression Formats Used in Sparse Workloads

Sparse matrices are the key ingredients of several application domains, from scientific computation to machine learning. The primary challenge with sparse matrices has been efficiently storing and transferring data, for which many sparse formats have been proposed to significantly eliminate zero entries. Such formats, essentially designed to optimize memory footprint, may not be as successful in performing faster processing. In other words, although they allow faster data transfer and improve memory bandwidth utilization -- the classic challenge of sparse problems -- their decompression mechanism can potentially create a computation bottleneck. Not only is this challenge not resolved, but also it becomes more serious with the advent of domain-specific architectures (DSAs), as they intend to more aggressively improve performance. The performance implications of using various formats along with DSAs, however, has not been extensively studied by prior work. To fill this gap of knowledge, we characterize the impact of using seven frequently used sparse formats on performance, based on a DSA for sparse matrix-vector multiplication (SpMV), implemented on an FPGA using high-level synthesis (HLS) tools, a growing and popular method for developing DSAs. Seeking a fair comparison, we tailor and optimize the HLS implementation of decompression for each format. We thoroughly explore diverse metrics, including decompression overhead, latency, balance ratio, throughput, memory bandwidth utilization, resource utilization, and power consumption, on a variety of real-world and synthetic sparse workloads.Comment: 11 pages, 14 figures, 2 table

High performance graph analysis on parallel architectures

PhD ThesisOver the last decade pharmacology has been developing computational methods to enhance drug development and testing. A computational method called network pharmacology uses graph analysis tools to determine protein target sets that can lead on better targeted drugs for diseases as Cancer. One promising area of network-based pharmacology is the detection of protein groups that can produce better e ects if they are targeted together by drugs. However, the e cient prediction of such protein combinations is still a bottleneck in the area of computational biology. The computational burden of the algorithms used by such protein prediction strategies to characterise the importance of such proteins consists an additional challenge for the eld of network pharmacology. Such computationally expensive graph algorithms as the all pairs shortest path (APSP) computation can a ect the overall drug discovery process as needed network analysis results cannot be given on time. An ideal solution for these highly intensive computations could be the use of super-computing. However, graph algorithms have datadriven computation dictated by the structure of the graph and this can lead to low compute capacity utilisation with execution times dominated by memory latency. Therefore, this thesis seeks optimised solutions for the real-world graph problems of critical node detection and e ectiveness characterisation emerged from the collaboration with a pioneer company in the eld of network pharmacology as part of a Knowledge Transfer Partnership (KTP) / Secondment (KTS). In particular, we examine how genetic algorithms could bene t the prediction of protein complexes where their removal could produce a more e ective 'druggable' impact. Furthermore, we investigate how the problem of all pairs shortest path (APSP) computation can be bene ted by the use of emerging parallel hardware architectures as GPU- and FPGA- desktop-based accelerators. In particular, we address the problem of critical node detection with the development of a heuristic search method. It is based on a genetic algorithm that computes optimised node combinations where their removal causes greater impact than common impact analysis strategies. Furthermore, we design a general pattern for parallel network analysis on multi-core architectures that considers graph's embedded properties. It is a divide and conquer approach that decomposes a graph into smaller subgraphs based on its strongly connected components and computes the all pairs shortest paths concurrently on GPU. Furthermore, we use linear algebra to design an APSP approach based on the BFS algorithm. We use algebraic expressions to transform the problem of path computation to multiple independent matrix-vector multiplications that are executed concurrently on FPGA. Finally, we analyse how the optimised solutions of perturbation analysis and parallel graph processing provided in this thesis will impact the drug discovery process.This research was part of a Knowledge Transfer Partnership (KTP) and Knowledge Transfer Secondment (KTS) between e-therapeutics PLC and Newcastle University. It was supported as a collaborative project by e-therapeutics PLC and Technology Strategy boar

FPGA-based Query Acceleration for Non-relational Databases

Database management systems are an integral part of today’s everyday life. Trends like smart applications, the internet of things, and business and social networks require applications to deal efficiently with data in various data models close to the underlying domain. Therefore, non-relational database systems provide a wide variety of database models, like graphs and documents. However, current non-relational database systems face performance challenges due to the end of Dennard scaling and therefore performance scaling of CPUs. In the meanwhile, FPGAs have gained traction as accelerators for data management. Our goal is to tackle the performance challenges of non-relational database systems with FPGA acceleration and, at the same time, address design challenges of FPGA acceleration itself. Therefore, we split this thesis up into two main lines of work: graph processing and flexible data processing. Because of the lacking benchmark practices for graph processing accelerators, we propose GraphSim. GraphSim is able to reproduce runtimes of these accelerators based on a memory access model of the approach. Through this simulation environment, we extract three performance-critical accelerator properties: asynchronous graph processing, compressed graph data structure, and multi-channel memory. Since these accelerator properties have not been combined in one system, we propose GraphScale. GraphScale is the first scalable, asynchronous graph processing accelerator working on a compressed graph and outperforms all state-of-the-art graph processing accelerators. Focusing on accelerator flexibility, we propose PipeJSON as the first FPGA-based JSON parser for arbitrary JSON documents. PipeJSON is able to achieve parsing at line-speed, outperforming the fastest, vectorized parsers for CPUs. Lastly, we propose the subgraph query processing accelerator GraphMatch which outperforms state-of-the-art CPU systems for subgraph query processing and is able to flexibly switch queries during runtime in a matter of clock cycles

Computing SpMV on FPGAs

There are hundreds of papers on accelerating sparse matrix vector multiplication (SpMV), however, only a handful target FPGAs. Some claim that FPGAs inherently perform inferiorly to CPUs and GPUs. FPGAs do perform inferiorly for some applications like matrix-matrix multiplication and matrix-vector multiplication. CPUs and GPUs have too much memory bandwidth and too much floating point computation power for FPGAs to compete. However, the low computations to memory operations ratio and irregular memory access of SpMV trips up both CPUs and GPUs. We see this as a leveling of the playing field for FPGAs. Our implementation focuses on three pillars: matrix traversal, multiply-accumulator design, and matrix compression. First, most SpMV implementations traverse the matrix in row-major order, but we mix column and row traversal. Second, To accommodate the new traversal the multiply accumulator stores many intermediate y values. Third, we compress the matrix to increase the transfer rate of the matrix from RAM to the FPGA. Together these pillars enable our SpMV implementation to perform competitively with CPUs and GPUs