Generating and auto-tuning parallel stencil codes

In this thesis, we present a software framework, Patus, which generates high performance stencil codes for different types of hardware platforms, including current multicore CPU and graphics processing unit architectures. The ultimate goals of the framework are productivity, portability (of both the code and performance), and achieving a high performance on the target platform. A stencil computation updates every grid point in a structured grid based on the values of its neighboring points. This class of computations occurs frequently in scientific and general purpose computing (e.g., in partial differential equation solvers or in image processing), justifying the focus on this kind of computation. The proposed key ingredients to achieve the goals of productivity, portability, and performance are domain specific languages (DSLs) and the auto-tuning methodology. The Patus stencil specification DSL allows the programmer to express a stencil computation in a concise way independently of hardware architecture-specific details. Thus, it increases the programmer productivity by disburdening her or him of low level programming model issues and of manually applying hardware platform-specific code optimization techniques. The use of domain specific languages also implies code reusability: once implemented, the same stencil specification can be reused on different hardware platforms, i.e., the specification code is portable across hardware architectures. Constructing the language to be geared towards a special purpose makes it amenable to more aggressive optimizations and therefore to potentially higher performance. Auto-tuning provides performance and performance portability by automated adaptation of implementation-specific parameters to the characteristics of the hardware on which the code will run. By automating the process of parameter tuning — which essentially amounts to solving an integer programming problem in which the objective function is the number representing the code's performance as a function of the parameter configuration, — the system can also be used more productively than if the programmer had to fine-tune the code manually. We show performance results for a variety of stencils, for which Patus was used to generate the corresponding implementations. The selection includes stencils taken from two real-world applications: a simulation of the temperature within the human body during hyperthermia cancer treatment and a seismic application. These examples demonstrate the framework's flexibility and ability to produce high performance code

상변화 메모리 시스템의 간섭 오류 완화 및 RMW 성능 향상 기법

학위논문(박사) -- 서울대학교대학원 : 공과대학 전기·정보공학부, 2021.8. 이혁재.Phase-change memory (PCM) announces the beginning of the new era of memory systems, owing to attractive characteristics. Many memory product manufacturers (e.g., Intel, SK Hynix, and Samsung) are developing related products. PCM can be applied to various circumstances; it is not simply limited to an extra-scale database. For example, PCM has a low standby power due to its non-volatility; hence, computation-intensive applications or mobile applications (i.e., long memory idle time) are suitable to run on PCM-based computing systems. Despite these fascinating features of PCM, PCM is still far from the general commercial market due to low reliability and long latency problems. In particular, low reliability is a painful problem for PCM in past decades. As the semiconductor process technology rapidly scales down over the years, DRAM reaches 10 nm class process technology. In addition, it is reported that the write disturbance error (WDE) would be a serious issue for PCM if it scales down below 54 nm class process technology. Therefore, addressing the problem of WDEs becomes essential to make PCM competitive to DRAM. To overcome this problem, this dissertation proposes a novel approach that can restore meta-stable cells on demand by levering two-level SRAM-based tables, thereby significantly reducing the number WDEs. Furthermore, a novel randomized approach is proposed to implement a replacement policy that originally requires hundreds of read ports on SRAM. The second problem of PCM is a long-latency compared to that of DRAM. In particular, PCM tries to enhance its throughput by adopting a larger transaction unit; however, the different unit size from the general-purpose processor cache line further degrades the system performance due to the introduction of a read-modify-write (RMW) module. Since there has never been any research related to RMW in a PCM-based memory system, this dissertation proposes a novel architecture to enhance the overall system performance and reliability of a PCM-based memory system having an RMW module. The proposed architecture enhances data re-usability without introducing extra storage resources. Furthermore, a novel operation that merges commands regardless of command types is proposed to enhance performance notably. Another problem is the absence of a full simulation platform for PCM. While the announced features of the PCM-related product (i.e., Intel Optane) are scarce due to confidential issues, all priceless information can be integrated to develop an architecture simulator that resembles the available product. To this end, this dissertation tries to scrape up all available features of modules in a PCM controller and implement a dedicated simulator for future research purposes.상변화 메모리는(PCM) 매력적인 특성을 통해 메모리 시스템의 새로운 시대의 시작을 알렸다. 많은 메모리 관련 제품 제조업체(예 : 인텔, SK 하이닉스, 삼성)가 관련 제품 개발에 박차를 가하고 있다. PCM은 단순히 대규모 데이터베이스에만 국한되지 않고 다양한 상황에 적용될 수 있다. 예를 들어, PCM은 비휘발성으로 인해 대기 전력이 낮다. 따라서 계산 집약적인 애플리케이션 또는 모바일 애플리케이션은(즉, 긴 메모리 유휴 시간) PCM 기반 컴퓨팅 시스템에서 실행하기에 적합하다. PCM의 이러한 매력적인 특성에도 불구하고 PCM은 낮은 신뢰성과 긴 대기 시간으로 인해 여전히 일반 산업 시장에서는 DRAM과 다소 격차가 있다. 특히 낮은 신뢰성은 지난 수십 년 동안 PCM 기술의 발전을 저해하는 문제다. 반도체 공정 기술이 수년에 걸쳐 빠르게 축소됨에 따라 DRAM은 10nm 급 공정 기술에 도달하였다. 이어서, 쓰기 방해 오류 (WDE)가 54nm 등급 프로세스 기술 아래로 축소되면 PCM에 심각한 문제가 될 것으로 보고되었다. 따라서, WDE 문제를 해결하는 것은 PCM이 DRAM과 동등한 경쟁력을 갖추도록 하는 데 있어 필수적이다. 이 문제를 극복하기 위해 이 논문에서는 2-레벨 SRAM 기반 테이블을 활용하여 WDE 수를 크게 줄여 필요에 따라 준 안정 셀을 복원할 수 있는 새로운 접근 방식을 제안한다. 또한, 원래 SRAM에서 수백 개의 읽기 포트가 필요한 대체 정책을 구현하기 위해 새로운 랜덤 기반의 기법을 제안한다. PCM의 두 번째 문제는 DRAM에 비해 지연 시간이 길다는 것이다. 특히 PCM은 더 큰 트랜잭션 단위를 채택하여 단위시간 당 데이터 처리량 향상을 도모한다. 그러나 범용 프로세서 캐시 라인과 다른 유닛 크기는 읽기-수정-쓰기 (RMW) 모듈의 도입으로 인해 시스템 성능을 저하하게 된다. PCM 기반 메모리 시스템에서 RMW 관련 연구가 없었기 때문에 본 논문은 RMW 모듈을 탑재 한 PCM 기반 메모리 시스템의 전반적인 시스템 성능과 신뢰성을 향상하게 시킬 수 있는 새로운 아키텍처를 제안한다. 제안된 아키텍처는 추가 스토리지 리소스를 도입하지 않고도 데이터 재사용성을 향상시킨다. 또한, 성능 향상을 위해 명령 유형과 관계없이 명령을 병합하는 새로운 작업을 제안한다. 또 다른 문제는 PCM을 위한 완전한 시뮬레이션 플랫폼이 부재하다는 것이다. PCM 관련 제품(예 : Intel Optane)에 대해 발표된 정보는 대외비 문제로 인해 부족하다. 하지만 알려져 있는 정보를 적절히 취합하면 시중 제품과 유사한 아키텍처 시뮬레이터를 개발할 수 있다. 이를 위해 본 논문은 PCM 메모리 컨트롤러에 필요한 모든 모듈 정보를 활용하여 향후 이와 관련된 연구에서 충분히 사용 가능한 전용 시뮬레이터를 구현하였다.1 INTRODUCTION 1 1.1 Limitation of Traditional Main Memory Systems 1 1.2 Phase-Change Memory as Main Memory 3 1.2.1 Opportunities of PCM-based System 3 1.2.2 Challenges of PCM-based System 4 1.3 Dissertation Overview 7 2 BACKGROUND AND PREVIOUS WORK 8 2.1 Phase-Change Memory 8 2.2 Mitigation Schemes for Write Disturbance Errors 10 2.2.1 Write Disturbance Errors 10 2.2.2 Verification and Correction 12 2.2.3 Lazy Correction 13 2.2.4 Data Encoding-based Schemes 14 2.2.5 Sparse-Insertion Write Cache 16 2.3 Performance Enhancement for Read-Modify-Write 17 2.3.1 Traditional Read-Modify-Write 17 2.3.2 Write Coalescing for RMW 19 2.4 Architecture Simulators for PCM 21 2.4.1 NVMain 21 2.4.2 Ramulator 22 2.4.3 DRAMsim3 22 3 IN-MODULE DISTURBANCE BARRIER 24 3.1 Motivation 25 3.2 IMDB: In Module-Disturbance Barrier 29 3.2.1 Architectural Overview 29 3.2.2 Implementation of Data Structures 30 3.2.3 Modification of Media Controller 36 3.3 Replacement Policy 38 3.3.1 Replacement Policy for IMDB 38 3.3.2 Approximate Lowest Number Estimator 40 3.4 Putting All Together: Case Studies 43 3.5 Evaluation 45 3.5.1 Configuration 45 3.5.2 Architectural Exploration 47 3.5.3 Effectiveness of the Replacement Policy 48 3.5.4 Sensitivity to Main Table Configuration 49 3.5.5 Sensitivity to Barrier Buffer Size 51 3.5.6 Sensitivity to AppLE Group Size 52 3.5.7 Comparison with Other Studies 54 3.6 Discussion 59 3.7 Summary 63 4 INTEGRATION OF AN RMW MODULE IN A PCM-BASED SYSTEM 64 4.1 Motivation 65 4.2 Utilization of DRAM Cache for RMW 67 4.2.1 Architectural Design 67 4.2.2 Algorithm 70 4.3 Typeless Command Merging 73 4.3.1 Architectural Design 73 4.3.2 Algorithm 74 4.4 An Alternative Implementation: SRC-RMW 78 4.4.1 Implementation of SRC-RMW 78 4.4.2 Design Constraint 80 4.5 Case Study 82 4.6 Evaluation 85 4.6.1 Configuration 85 4.6.2 Speedup 88 4.6.3 Read Reliability 91 4.6.4 Energy Consumption: Selecting a Proper Page Size 93 4.6.5 Comparison with Other Studies 95 4.7 Discussion 97 4.8 Summary 99 5 AN ALL-INCLUSIVE SIMULATOR FOR A PCM CONTROLLER 100 5.1 Motivation 101 5.2 PCMCsim: PCM Controller Simulator 103 5.2.1 Architectural Overview 103 5.2.2 Underlying Classes of PCMCsim 104 5.2.3 Implementation of Contention Behavior 108 5.2.4 Modules of PCMCsim 109 5.3 Evaluation 116 5.3.1 Correctness of the Simulator 116 5.3.2 Comparison with Other Simulators 117 5.4 Summary 119 6 Conclusion 120 Abstract (In Korean) 141 Acknowledgment 143박

Techniques of design optimisation for algorithms implemented in software

The overarching objective of this thesis was to develop tools for parallelising, optimising, and implementing algorithms on parallel architectures, in particular General Purpose Graphics Processors (GPGPUs). Two projects were chosen from different application areas in which GPGPUs are used: a defence application involving image compression, and a modelling application in bioinformatics (computational immunology). Each project had its own specific objectives, as well as supporting the overall research goal. The defence / image compression project was carried out in collaboration with the Jet Propulsion Laboratories. The specific questions were: to what extent an algorithm designed for bit-serial for the lossless compression of hyperspectral images on-board unmanned vehicles (UAVs) in hardware could be parallelised, whether GPGPUs could be used to implement that algorithm, and whether a software implementation with or without GPGPU acceleration could match the throughput of a dedicated hardware (FPGA) implementation. The dependencies within the algorithm were analysed, and the algorithm parallelised. The algorithm was implemented in software for GPGPU, and optimised. During the optimisation process, profiling revealed less than optimal device utilisation, but no further optimisations resulted in an improvement in speed. The design had hit a local-maximum of performance. Analysis of the arithmetic intensity and data-flow exposed flaws in the standard optimisation metric of kernel occupancy used for GPU optimisation. Redesigning the implementation with revised criteria (fused kernels, lower occupancy, and greater data locality) led to a new implementation with 10x higher throughput. GPGPUs were shown to be viable for on-board implementation of the CCSDS lossless hyperspectral image compression algorithm, exceeding the performance of the hardware reference implementation, and providing sufficient throughput for the next generation of image sensor as well. The second project was carried out in collaboration with biologists at the University of Arizona and involved modelling a complex biological system – VDJ recombination involved in the formation of T-cell receptors (TCRs). Generation of immune receptors (T cell receptor and antibodies) by VDJ recombination is an enormously complex process, which can theoretically synthesize greater than 1018 variants. Originally thought to be a random process, the underlying mechanisms clearly have a non-random nature that preferentially creates a small subset of immune receptors in many individuals. Understanding this bias is a longstanding problem in the field of immunology. Modelling the process of VDJ recombination to determine the number of ways each immune receptor can be synthesized, previously thought to be untenable, is a key first step in determining how this special population is made. The computational tools developed in this thesis have allowed immunologists for the first time to comprehensively test and invalidate a longstanding theory (convergent recombination) for how this special population is created, while generating the data needed to develop novel hypothesis

상변화 메모리 시스템의 간섭 오류 완화 및 RMW 성능 향상 기법

학위논문(박사)--서울대학교 대학원 :공과대학 전기·정보공학부,2021. 8. 이혁재.Phase-change memory (PCM) announces the beginning of the new era of memory systems, owing to attractive characteristics. Many memory product manufacturers (e.g., Intel, SK Hynix, and Samsung) are developing related products. PCM can be applied to various circumstances; it is not simply limited to an extra-scale database. For example, PCM has a low standby power due to its non-volatility; hence, computation-intensive applications or mobile applications (i.e., long memory idle time) are suitable to run on PCM-based computing systems. The second problem of PCM is a long-latency compared to that of DRAM. In particular, PCM tries to enhance its throughput by adopting a larger transaction unit; however, the different unit size from the general-purpose processor cache line further degrades the system performance due to the introduction of a read-modify-write (RMW) module. Since there has never been any research related to RMW in a PCM-based memory system, this dissertation proposes a novel architecture to enhance the overall system performance and reliability of a PCM-based memory system having an RMW module. The proposed architecture enhances data re-usability without introducing extra storage resources. Furthermore, a novel operation that merges commands regardless of command types is proposed to enhance performance notably.Despite these fascinating features of PCM, PCM is still far from the general commercial market due to low reliability and long latency problems. In particular, low reliability is a painful problem for PCM in past decades. As the semiconductor process technology rapidly scales down over the years, DRAM reaches 10 nm class process technology. In addition, it is reported that the write disturbance error (WDE) would be a serious issue for PCM if it scales down below 54 nm class process technology. Therefore, addressing the problem of WDEs becomes essential to make PCM competitive to DRAM. To overcome this problem, this dissertation proposes a novel approach that can restore meta-stable cells on demand by levering two-level SRAM-based tables, thereby significantly reducing the number WDEs. Furthermore, a novel randomized approach is proposed to implement a replacement policy that originally requires hundreds of read ports on SRAM.Another problem is the absence of a full simulation platform for PCM. While the announced features of the PCM-related product (i.e., Intel Optane) are scarce due to confidential issues, all priceless information can be integrated to develop an architecture simulator that resembles the available product. To this end, this dissertation tries to scrape up all available features of modules in a PCM controller and implement a dedicated simulator for future research purposes

Towards Computational Efficiency of Next Generation Multimedia Systems

To address throughput demands of complex applications (like Multimedia), a next-generation system designer needs to co-design and co-optimize the hardware and software layers. Hardware/software knobs must be tuned in synergy to increase the throughput efficiency. This thesis provides such algorithmic and architectural solutions, while considering the new technology challenges (power-cap and memory aging). The goal is to maximize the throughput efficiency, under timing- and hardware-constraints

A configurable vector processor for accelerating speech coding algorithms

The growing demand for voice-over-packer (VoIP) services and multimedia-rich applications has made increasingly important the efficient, real-time implementation of low-bit rates speech coders on embedded VLSI platforms. Such speech coders are designed to substantially reduce the bandwidth requirements thus enabling dense multichannel gateways in small form factor. This however comes at a high computational cost which mandates the use of very high performance embedded processors. This thesis investigates the potential acceleration of two major ITU-T speech coding algorithms, namely G.729A and G.723.1, through their efficient implementation on a configurable extensible vector embedded CPU architecture. New scalar and vector ISAs were introduced which resulted in up to 80% reduction in the dynamic instruction count of both workloads. These instructions were subsequently encapsulated into a parametric, hybrid SISD (scalar processor)–SIMD (vector) processor. This work presents the research and implementation of the vector datapath of this vector coprocessor which is tightly-coupled to a Sparc-V8 compliant CPU, the optimization and simulation methodologies employed and the use of Electronic System Level (ESL) techniques to rapidly design SIMD datapaths

Optimizing AI at the Edge: from network topology design to MCU deployment

The first topic analyzed in the thesis will be Neural Architecture Search (NAS). I will focus on two different tools that I developed, one to optimize the architecture of Temporal Convolutional Networks (TCNs), a convolutional model for time-series processing that has recently emerged, and one to optimize the data precision of tensors inside CNNs. The first NAS proposed explicitly targets the optimization of the most peculiar architectural parameters of TCNs, namely dilation, receptive field, and the number of features in each layer. Note that this is the first NAS that explicitly targets these networks. The second NAS proposed instead focuses on finding the most efficient data format for a target CNN, with the granularity of the layer filter. Note that applying these two NASes in sequence allows an "application designer" to minimize the structure of the neural network employed, minimizing the number of operations or the memory usage of the network. After that, the second topic described is the optimization of neural network deployment on edge devices. Importantly, exploiting edge platforms' scarce resources is critical for NN efficient execution on MCUs. To do so, I will introduce DORY (Deployment Oriented to memoRY) -- an automatic tool to deploy CNNs on low-cost MCUs. DORY, in different steps, can manage different levels of memory inside the MCU automatically, offload the computation workload (i.e., the different layers of a neural network) to dedicated hardware accelerators, and automatically generates ANSI C code that orchestrates off- and on-chip transfers with the computation phases. On top of this, I will introduce two optimized computation libraries that DORY can exploit to deploy TCNs and Transformers on edge efficiently. I conclude the thesis with two different applications on bio-signal analysis, i.e., heart rate tracking and sEMG-based gesture recognition

Systematic Design Methods for Efficient Off-Chip DRAM Access

Typical design flows for digital hardware take, as their input, an abstract description of computation and data transfer between logical memories. No existing commercial high-level synthesis tool demonstrates the ability to map logical memory inferred from a high level language to external memory resources. This thesis develops techniques for doing this, specifically targeting off-chip dynamic memory (DRAM) devices. These are a commodity technology in widespread use with standardised interfaces. In use, the bandwidth of an external memory interface and the latency of memory requests asserted on it may become the bottleneck limiting the performance of a hardware design. Careful consideration of this is especially important when designing with DRAMs, whose latency and bandwidth characteristics depend upon the sequence of memory requests issued by a controller. Throughout the work presented here, we pursue exact compile-time methods for designing application-specific memory systems with a focus on guaranteeing predictable performance through static analysis. This contrasts with much of the surveyed existing work, which considers general purpose memory controllers and optimized policies which improve performance in experiments run using simulation of suites of benchmark codes. The work targets loop-nests within imperative source code, extracting a mathematical representation of the loop-nest statements and their associated memory accesses, referred to as the ‘Polytope Model’. We extend this mathematical representation to represent the physical DRAM ‘row’ and ‘column’ structures accessed when performing memory transfers. From this augmented representation, we can automatically derive DRAM controllers which buffer data in on-chip memory and transfer data in an efficient order. Buffering data and exploiting ‘reuse’ of data is shown to enable up to 50× reduction in the quantity of data transferred to external memory. The reordering of memory transactions exploiting knowledge of the physical layout of the DRAM device allowing to 4× improvement in the efficiency of those data transfers

Software for Exascale Computing - SPPEXA 2016-2019

This open access book summarizes the research done and results obtained in the second funding phase of the Priority Program 1648 "Software for Exascale Computing" (SPPEXA) of the German Research Foundation (DFG) presented at the SPPEXA Symposium in Dresden during October 21-23, 2019. In that respect, it both represents a continuation of Vol. 113 in Springer’s series Lecture Notes in Computational Science and Engineering, the corresponding report of SPPEXA’s first funding phase, and provides an overview of SPPEXA’s contributions towards exascale computing in today's sumpercomputer technology. The individual chapters address one or more of the research directions (1) computational algorithms, (2) system software, (3) application software, (4) data management and exploration, (5) programming, and (6) software tools. The book has an interdisciplinary appeal: scholars from computational sub-fields in computer science, mathematics, physics, or engineering will find it of particular interest