GPUs as Storage System Accelerators

Massively multicore processors, such as Graphics Processing Units (GPUs), provide, at a comparable price, a one order of magnitude higher peak performance than traditional CPUs. This drop in the cost of computation, as any order-of-magnitude drop in the cost per unit of performance for a class of system components, triggers the opportunity to redesign systems and to explore new ways to engineer them to recalibrate the cost-to-performance relation. This project explores the feasibility of harnessing GPUs' computational power to improve the performance, reliability, or security of distributed storage systems. In this context, we present the design of a storage system prototype that uses GPU offloading to accelerate a number of computationally intensive primitives based on hashing, and introduce techniques to efficiently leverage the processing power of GPUs. We evaluate the performance of this prototype under two configurations: as a content addressable storage system that facilitates online similarity detection between successive versions of the same file and as a traditional system that uses hashing to preserve data integrity. Further, we evaluate the impact of offloading to the GPU on competing applications' performance. Our results show that this technique can bring tangible performance gains without negatively impacting the performance of concurrently running applications.Comment: IEEE Transactions on Parallel and Distributed Systems, 201

Evaluating Erasure Codes in Dicoogle PACS

DICOM (Digital Imaging and Communication in Medicine) is a standard for image and data transmission in medical purpose hardware and is commonly used for viewing, storing, printing and transmitting images. As a part of the way that DICOM transmits files, the PACS (Picture Archiving and Communication System) platform, Dicoogle, has become one of the most in-demand image processing and viewing platforms. However, the Dicoogle PACS architecture does not guarantee image information recovery in the case of information loss. Therefore, this paper proposes a file recovery solution in the Dicoogle architecture. The proposal consists of maximizing the encoding and decoding performance of medical images through computational parallelism. To validate the proposal, the Java programming language based on the Reed-Solomon algorithm is implemented in different performance tests. The experimental results show that the proposal is optimal in terms of image processing time for the Dicoogle PACS storage system.Ministry of Science, Innovation and Universities (MICINN) of Spain PGC2018 098883-B-C44European CommissionPrograma para el Desarrollo Profesional Docente para el Tipo Superior (PRODEP) of MexicoCorporacion Ecuatoriana para el Desarrollo de la Investigacion y la Academia (CEDIA) of Ecuador CEPRA XII-2018-13Universidad de Las Americas (UDLA), Quito, Ecuador IEA.WHP.21.0

An erasure-resilient and compute-efficient coding scheme for storage applications

Driven by rapid technological advancements, the amount of data that is created, captured, communicated, and stored worldwide has grown exponentially over the past decades. Along with this development it has become critical for many disciplines of science and business to being able to gather and analyze large amounts of data. The sheer volume of the data often exceeds the capabilities of classical storage systems, with the result that current large-scale storage systems are highly distributed and are comprised of a high number of individual storage components. As with any other electronic device, the reliability of storage hardware is governed by certain probability distributions, which in turn are influenced by the physical processes utilized to store the information. The traditional way to deal with the inherent unreliability of combined storage systems is to replicate the data several times. Another popular approach to achieve failure tolerance is to calculate the block-wise parity in one or more dimensions. With better understanding of the different failure modes of storage components, it has become evident that sophisticated high-level error detection and correction techniques are indispensable for the ever-growing distributed systems. The utilization of powerful cyclic error-correcting codes, however, comes with a high computational penalty, since the required operations over finite fields do not map very well onto current commodity processors. This thesis introduces a versatile coding scheme with fully adjustable fault-tolerance that is tailored specifically to modern processor architectures. To reduce stress on the memory subsystem the conventional table-based algorithm for multiplication over finite fields has been replaced with a polynomial version. This arithmetically intense algorithm is better suited to the wide SIMD units of the currently available general purpose processors, but also displays significant benefits when used with modern many-core accelerator devices (for instance the popular general purpose graphics processing units). A CPU implementation using SSE and a GPU version using CUDA are presented. The performance of the multiplication depends on the distribution of the polynomial coefficients in the finite field elements. This property has been used to create suitable matrices that generate a linear systematic erasure-correcting code which shows a significantly increased multiplication performance for the relevant matrix elements. Several approaches to obtain the optimized generator matrices are elaborated and their implications are discussed. A Monte-Carlo-based construction method allows it to influence the specific shape of the generator matrices and thus to adapt them to special storage and archiving workloads. Extensive benchmarks on CPU and GPU demonstrate the superior performance and the future application scenarios of this novel erasure-resilient coding scheme

Doctor of Philosophy

dissertationAs the base of the software stack, system-level software is expected to provide ecient and scalable storage, communication, security and resource management functionalities. However, there are many computationally expensive functionalities at the system level, such as encryption, packet inspection, and error correction. All of these require substantial computing power. What's more, today's application workloads have entered gigabyte and terabyte scales, which demand even more computing power. To solve the rapidly increased computing power demand at the system level, this dissertation proposes using parallel graphics pro- cessing units (GPUs) in system software. GPUs excel at parallel computing, and also have a much faster development trend in parallel performance than central processing units (CPUs). However, system-level software has been originally designed to be latency-oriented. GPUs are designed for long-running computation and large-scale data processing, which are throughput-oriented. Such mismatch makes it dicult to t the system-level software with the GPUs. This dissertation presents generic principles of system-level GPU computing developed during the process of creating our two general frameworks for integrating GPU computing in storage and network packet processing. The principles are generic design techniques and abstractions to deal with common system-level GPU computing challenges. Those principles have been evaluated in concrete cases including storage and network packet processing applications that have been augmented with GPU computing. The signicant performance improvement found in the evaluation shows the eectiveness and eciency of the proposed techniques and abstractions. This dissertation also presents a literature survey of the relatively young system-level GPU computing area, to introduce the state of the art in both applications and techniques, and also their future potentials

A checkpointing mechanism for GPU intensive HPC applications

Please refer to pdf.James Watt ScholarshipEngineering and Physical Sciences Research Council (EPSRC) grants EP/N028201/1 and EP/L00058X/

ACCELERATING STORAGE APPLICATIONS WITH EMERGING KEY VALUE STORAGE DEVICES

With the continuous data explosion in the big data era, traditional software and hardware stack are facing unprecedented challenges on how to operate on such data scale. Thus, designing new architectures and efficient systems for data oriented applications has become increasingly critical. This motivates us to re-think of the conventional storage system design and re-architect both software and hardware to meet the challenges of scale. Besides the fast growth of data volume, the increasing demand on storage applications such as video streaming, data analytics are pushing high performance flash based storage devices to replace the traditional spinning disks. Such all-flash era increase the data reliability concerns due to the endurance problem of flash devices. Key-value stores (KVS) are important storage infrastructure to handle the fast growing unstructured data and have been widely deployed in a variety of scale-out enterprise applications such as online retail, big data analytic, social networks, etc. How to efficiently manage data redundancy for key-value stores to provide data reliability, how to efficiently support range query for key-value stores to accelerate analytic oriented applications under emerging key-value store system architecture become an important research problem. In this research, we focus on how to design new software hardware architectures for the keyvalue store applications to provide reliability and improve query performance. In order to address the different issues identified in this dissertation, we propose to employ a logical key management layer, a thin layer above the KV devices that maps logical keys into phsyical keys on the devices. We show how such a layer can enable multiple solutions to improve the performance and reliability of KVSSD based storage systems. First, we present KVRAID, a high performance, write efficient erasure coding management scheme on emerging key-value SSDs. The core innovation of KVRAID is to propose a logical key management layer that maps logical keys to physical keys to efficiently pack similar size KV objects and dynamically manage the membership of erasure coding groups. Unlike existing schemes which manage erasure codes on the block level, KVRAID manages the erasure codes on the KV object level. In order to achieve better storage efficiency for variable sized objects, KVRAID predefines multiple fixed sizes (slabs) according to the object size distribution for the erasure code. KVRAID uses a logical to physical key conversion to pack the KV objects of similar size into a parity group. KVRAID uses a lazy deletion mechanism with a garbage collector for object updates. Our experiments show that in 100% put case, KVRAID outperforms software block RAID by 18x in case of throughput and reduces 15x write amplification (WAF) with only ~5% CPU utilization. In a mixed update/get workloads, KVRAID achieves ~4x better throughput with ~23% CPU utilization and reduces the storage overhead and WAF by 3.6x and 11.3x in average respectively. Second, we present KVRangeDB, an ordered log structure tree based key index that supports range queries on a hash-based KVSSD. In addition, we propose to pack smaller application records into a larger physical record on the device through the logical key management layer. We compared the performance of KVRangeDB against RocksDB implementation on KVSSD and stateof- art software KV-store Wisckey on block device, on three types of real world applications of cloud-serving workloads, TABLEFS filesystem and time-series databases. For cloud serving applications, KVRangeDB achieves 8.3x and 1.7x better 99.9% write tail latency respectively compared to RocksDB implementation on KV-SSD and Wisckey on block SSD. On the query side, KVrangeDB only performs worse for those very long scans, but provides fast point queries and closed range queries. The experiments on TABLEFS demonstrate that using KVRangeDB for metadata indexing can boost the performance by a factor of ~6.3x in average and reduce ~3.9x CPU cost for four metadata-intensive workloads compared to RocksDB implementation on KVSSD. Compared toWisckey, KVRangeDB improves performance by ~2.6x in average and reduces ~1.7x CPU usage. Third, we propose a generic FPGA accelerator for emerging Minimum Storage Regenerating (MSR) codes encoding/decoding which maximizes the computation parallelism and minimizes the data movement between off-chip DRAM and the on-chip SRAM buffers. To demonstrate the efficiency of our proposed accelerator, we implemented the encoding/decoding algorithms for a specific MSR code called Zigzag code on Xilinx VCU1525 acceleration card. Our evaluation shows our proposed accelerator can achieve ~2.4-3.1x better throughput and ~4.2-5.7x better power efficiency compared to the state-of-art multi-core CPU implementation and ~2.8-3.3x better throughput and ~4.2-5.3x better power efficiency compared to a modern GPU accelerato