낸드 플래시 저장장치의 성능 및 수명 향상을 위한 프로그램 컨텍스트 기반 최적화 기법

학위논문 (박사)-- 서울대학교 대학원 : 공과대학 컴퓨터공학부, 2019. 2. 김지홍.컴퓨팅 시스템의 성능 향상을 위해, 기존의 느린 하드디스크(HDD)를 빠른 낸드 플래시 메모리 기반 저장장치(SSD)로 대체하고자 하는 연구가 최근 활발히 진행 되고 있다. 그러나 지속적인 반도체 공정 스케일링 및 멀티 레벨링 기술로 SSD 가격을 동급 HDD 수준으로 낮아졌지만, 최근의 첨단 디바이스 기술의 부작용으 로 NAND 플래시 메모리의 수명이 짧아지는 것은 고성능 컴퓨팅 시스템에서의 SSD의 광범위한 채택을 막는 주요 장벽 중 하나이다. 본 논문에서는 최근의 고밀도 낸드 플래시 메모리의 수명 및 성능 문제를 해결하기 위한 시스템 레벨의 개선 기술을 제안한다. 제안 된 기법은 응용 프로 그램의 쓰기 문맥을 활용하여 기존에는 얻을 수 없었던 데이터 수명 패턴 및 중복 데이터 패턴을 분석하였다. 이에 기반하여, 단일 계층의 단순한 정보만을 활용했 던 기존 기법의 한계를 극복함으로써 효과적으로 NAND 플래시 메모리의 성능 및 수명을 향상시키는 최적화 방법론을 제시한다. 먼저, 응용 프로그램의 I/O 작업에는 문맥에 따라 고유한 데이터 수명과 중 복 데이터의 패턴이 존재한다는 점을 분석을 통해 확인하였다. 문맥 정보를 효과 적으로 활용하기 위해 프로그램 컨텍스트 (쓰기 문맥) 추출 방법을 구현 하였다. 프로그램 컨텍스트 정보를 통해 가비지 컬렉션 부하와 제한된 수명의 NAND 플 래시 메모리 개선을 위한 기존 기술의 한계를 효과적으로 극복할 수 있다. 둘째, 멀티 스트림 SSD에서 WAF를 줄이기 위해 데이터 수명 예측의 정확 성을 높이는 기법을 제안하였다. 이를 위해 애플리케이션의 I/O 컨텍스트를 활용 하는 시스템 수준의 접근 방식을 제안하였다. 제안된 기법의 핵심 동기는 데이터 수명이 LBA보다 높은 추상화 수준에서 평가 되어야 한다는 것이다. 따라서 프 로그램 컨텍스트를 기반으로 데이터의 수명을 보다 정확히 예측함으로써, 기존 기법에서 LBA를 기반으로 데이터 수명을 관리하는 한계를 극복한다. 결론적으 로 따라서 가비지 컬렉션의 효율을 높이기 위해 수명이 짧은 데이터를 수명이 긴 데이터와 효과적으로 분리 할 수 있다. 마지막으로, 쓰기 프로그램 컨텍스트의 중복 데이터 패턴 분석을 기반으로 불필요한 중복 제거 작업을 피할 수있는 선택적 중복 제거를 제안한다. 중복 데 이터를 생성하지 않는 프로그램 컨텍스트가 존재함을 분석적으로 보이고 이들을 제외함으로써, 중복제거 동작의 효율성을 높일 수 있다. 또한 중복 데이터가 발생 하는 패턴에 기반하여 기록된 데이터를 관리하는 자료구조 유지 정책을 새롭게 제안하였다. 추가적으로, 서브 페이지 청크를 도입하여 중복 데이터를 제거 할 가능성을 높이는 세분화 된 중복 제거를 제안한다. 제안 된 기술의 효과를 평가하기 위해 다양한 실제 시스템에서 수집 된 I/O 트레이스에 기반한 시뮬레이션 평가 뿐만 아니라 에뮬레이터 구현을 통해 실제 응용을 동작하면서 일련의 평가를 수행했다. 더 나아가 멀티 스트림 디바이스의 내부 펌웨어를 수정하여 실제와 가장 비슷하게 설정된 환경에서 실험을 수행하 였다. 실험 결과를 통해 제안된 시스템 수준 최적화 기법이 성능 및 수명 개선 측면에서 기존 최적화 기법보다 더 효과적이었음을 확인하였다. 향후 제안된 기 법들이 보다 더 발전된다면, 낸드 플래시 메모리가 초고속 컴퓨팅 시스템의 주 저장장치로 널리 사용되는 데에 긍정적인 기여를 할 수 있을 것으로 기대된다.Replacing HDDs with NAND flash-based storage devices (SSDs) has been one of the major challenges in modern computing systems especially in regards to better performance and higher mobility. Although the continuous semiconductor process scaling and multi-leveling techniques lower the price of SSDs to the comparable level of HDDs, the decreasing lifetime of NAND flash memory, as a side effect of recent advanced device technologies, is emerging as one of the major barriers to the wide adoption of SSDs in highperformance computing systems. In this dissertation, system-level lifetime improvement techniques for recent high-density NAND flash memory are proposed. Unlike existing techniques, the proposed techniques resolve the problems of decreasing performance and lifetime of NAND flash memory by exploiting the I/O context of an application to analyze data lifetime patterns or duplicate data contents patterns. We first present that I/O activities of an application have distinct data lifetime and duplicate data patterns. In order to effectively utilize the context information, we implemented the program context extraction method. With the program context, we can overcome the limitations of existing techniques for improving the garbage collection overhead and limited lifetime of NAND flash memory. Second, we propose a system-level approach to reduce WAF that exploits the I/O context of an application to increase the data lifetime prediction for the multi-streamed SSDs. The key motivation behind the proposed technique was that data lifetimes should be estimated at a higher abstraction level than LBAs, so we employ a write program context as a stream management unit. Thus, it can effectively separate data with short lifetimes from data with long lifetimes to improve the efficiency of garbage collection. Lastly, we propose a selective deduplication that can avoid unnecessary deduplication work based on the duplicate data pattern analysis of write program context. With the help of selective deduplication, we also propose fine-grained deduplication which improves the likelihood of eliminating redundant data by introducing sub-page chunk. It also resolves technical difficulties caused by its finer granularity, i.e., increased memory requirement and read response time. In order to evaluate the effectiveness of the proposed techniques, we performed a series of evaluations using both a trace-driven simulator and emulator with I/O traces which were collected from various real-world systems. To understand the feasibility of the proposed techniques, we also implemented them in Linux kernel on top of our in-house flash storage prototype and then evaluated their effects on the lifetime while running real-world applications. Our experimental results show that system-level optimization techniques are more effective over existing optimization techniques.I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1.1 Garbage Collection Problem . . . . . . . . . . . . . 2 1.1.2 Limited Endurance Problem . . . . . . . . . . . . . 4 1.2 Dissertation Goals . . . . . . . . . . . . . . . . . . . . . . . 5 1.3 Contributions . . . . . . . . . . . . . . . . . . . . . . . . . 6 1.4 Dissertation Structure . . . . . . . . . . . . . . . . . . . . . 7 II. Background . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.1 NAND Flash Memory System Software . . . . . . . . . . . 9 2.2 NAND Flash-Based Storage Devices . . . . . . . . . . . . . 10 2.3 Multi-stream Interface . . . . . . . . . . . . . . . . . . . . 11 2.4 Inline Data Deduplication Technique . . . . . . . . . . . . . 12 2.5 Related Work . . . . . . . . . . . . . . . . . . . . . . . . . 13 2.5.1 Data Separation Techniques for Multi-streamed SSDs 13 2.5.2 Write Traffic Reduction Techniques . . . . . . . . . 15 2.5.3 Program Context based Optimization Techniques for Operating Systems . . . . . . . . 18 III. Program Context-based Analysis . . . . . . . . . . . . . . . . 21 3.1 Definition and Extraction of Program Context . . . . . . . . 21 3.2 Data Lifetime Patterns of I/O Activities . . . . . . . . . . . 24 3.3 Duplicate Data Patterns of I/O Activities . . . . . . . . . . . 26 IV. Fully Automatic Stream Management For Multi-Streamed SSDs Using Program Contexts . . 29 4.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 4.2 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 4.2.1 No Automatic Stream Management for General I/O Workloads . . . . . . . . . 33 4.2.2 Limited Number of Supported Streams . . . . . . . 36 4.3 Automatic I/O Activity Management . . . . . . . . . . . . . 38 4.3.1 PC as a Unit of Lifetime Classification for General I/O Workloads . . . . . . . . . . . 39 4.4 Support for Large Number of Streams . . . . . . . . . . . . 41 4.4.1 PCs with Large Lifetime Variances . . . . . . . . . 42 4.4.2 Implementation of Internal Streams . . . . . . . . . 44 4.5 Design and Implementation of PCStream . . . . . . . . . . 46 4.5.1 PC Lifetime Management . . . . . . . . . . . . . . 46 4.5.2 Mapping PCs to SSD streams . . . . . . . . . . . . 49 4.5.3 Internal Stream Management . . . . . . . . . . . . . 50 4.5.4 PC Extraction for Indirect Writes . . . . . . . . . . 51 4.6 Experimental Results . . . . . . . . . . . . . . . . . . . . . 53 4.6.1 Experimental Settings . . . . . . . . . . . . . . . . 53 4.6.2 Performance Evaluation . . . . . . . . . . . . . . . 55 4.6.3 WAF Comparison . . . . . . . . . . . . . . . . . . . 56 4.6.4 Per-stream Lifetime Distribution Analysis . . . . . . 57 4.6.5 Impact of Internal Streams . . . . . . . . . . . . . . 58 4.6.6 Impact of the PC Attribute Table . . . . . . . . . . . 60 V. Deduplication Technique using Program Contexts . . . . . . 62 5.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 5.2 Selective Deduplication using Program Contexts . . . . . . . 63 5.2.1 PCDedup: Improving SSD Deduplication Efficiency using Selective Hash Cache Management . . . . . . 63 5.2.2 2-level LRU Eviction Policy . . . . . . . . . . . . . 68 5.3 Exploiting Small Chunk Size . . . . . . . . . . . . . . . . . 70 5.3.1 Fine-Grained Deduplication . . . . . . . . . . . . . 70 5.3.2 Read Overhead Management . . . . . . . . . . . . . 76 5.3.3 Memory Overhead Management . . . . . . . . . . . 80 5.3.4 Experimental Results . . . . . . . . . . . . . . . . . 82 VI. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 6.1 Summary and Conclusions . . . . . . . . . . . . . . . . . . 88 6.2 Future Work . . . . . . . . . . . . . . . . . . . . . . . . . . 89 6.2.1 Supporting applications that have unusal program contexts . . . . . . . . . . . . . 89 6.2.2 Optimizing read request based on the I/O context . . 90 6.2.3 Exploiting context information to improve fingerprint lookups . . . . .. . . . . . 91 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92Docto

Updates in metabolomics tools and resources: 2014-2015

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources—in the form of tools, software, and databases—is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table

Remedies Brief of Amici Curiae

None.

Effective memory management for mobile environments

Smartphones, tablets, and other mobile devices exhibit vastly different constraints compared to regular or classic computing environments like desktops, laptops, or servers. Mobile devices run dozens of so-called “apps” hosted by independent virtual machines (VM). All these VMs run concurrently and each VM deploys purely local heuristics to organize resources like memory, performance, and power. Such a design causes conflicts across all layers of the software stack, calling for the evaluation of VMs and the optimization techniques specific for mobile frameworks. In this dissertation, we study the design of managed runtime systems for mobile platforms. More specifically, we deepen the understanding of interactions between garbage collection (GC) and system layers. We develop tools to monitor the memory behavior of Android-based apps and to characterize GC performance, leading to the development of new techniques for memory management that address energy constraints, time performance, and responsiveness. We implement a GC-aware frequency scaling governor for Android devices. We also explore the tradeoffs of power and performance in vivo for a range of realistic GC variants, with established benchmarks and real applications running on Android virtual machines. We control for variation due to dynamic voltage and frequency scaling (DVFS), Just-in-time (JIT) compilation, and across established dimensions of heap memory size and concurrency. Finally, we provision GC as a global service that collects statistics from all running VMs and then makes an informed decision that optimizes across all them (and not just locally), and across all layers of the stack. Our evaluation illustrates the power of such a central coordination service and garbage collection mechanism in improving memory utilization, throughput, and adaptability to user activities. In fact, our techniques aim at a sweet spot, where total on-chip energy is reduced (20–30%) with minimal impact on throughput and responsiveness (5–10%). The simplicity and efficacy of our approach reaches well beyond the usual optimization techniques

Overcoming Language Dichotomies: Toward Effective Program Comprehension for Mobile App Development

Mobile devices and platforms have become an established target for modern software developers due to performant hardware and a large and growing user base numbering in the billions. Despite their popularity, the software development process for mobile apps comes with a set of unique, domain-specific challenges rooted in program comprehension. Many of these challenges stem from developer difficulties in reasoning about different representations of a program, a phenomenon we define as a "language dichotomy". In this paper, we reflect upon the various language dichotomies that contribute to open problems in program comprehension and development for mobile apps. Furthermore, to help guide the research community towards effective solutions for these problems, we provide a roadmap of directions for future work.Comment: Invited Keynote Paper for the 26th IEEE/ACM International Conference on Program Comprehension (ICPC'18

Models and metaphors: complexity theory and through-life management in the built environment

Complexity thinking may have both modelling and metaphorical applications in the through-life management of the built environment. These two distinct approaches are examined and compared. In the first instance, some of the sources of complexity in the design, construction and maintenance of the built environment are identified. The metaphorical use of complexity in management thinking and its application in the built environment are briefly examined. This is followed by an exploration of modelling techniques relevant to built environment concerns. Non-linear and complex mathematical techniques such as fuzzy logic, cellular automata and attractors, may be applicable to their analysis. Existing software tools are identified and examples of successful built environment applications of complexity modelling are given. Some issues that arise include the definition of phenomena in a mathematically usable way, the functionality of available software and the possibility of going beyond representational modelling. Further questions arising from the application of complexity thinking are discussed, including the possibilities for confusion that arise from the use of metaphor. The metaphor of a 'commentary machine' is suggested as a possible way forward and it is suggested that an appropriate linguistic analysis can in certain situations reduce perceived complexity

The Sensor Network Workbench: Towards Functional Specification, Verification and Deployment of Constrained Distributed Systems

As the commoditization of sensing, actuation and communication hardware increases, so does the potential for dynamically tasked sense and respond networked systems (i.e., Sensor Networks or SNs) to replace existing disjoint and inflexible special-purpose deployments (closed-circuit security video, anti-theft sensors, etc.). While various solutions have emerged to many individual SN-centric challenges (e.g., power management, communication protocols, role assignment), perhaps the largest remaining obstacle to widespread SN deployment is that those who wish to deploy, utilize, and maintain a programmable Sensor Network lack the programming and systems expertise to do so. The contributions of this thesis centers on the design, development and deployment of the SN Workbench (snBench). snBench embodies an accessible, modular programming platform coupled with a flexible and extensible run-time system that, together, support the entire life-cycle of distributed sensory services. As it is impossible to find a one-size-fits-all programming interface, this work advocates the use of tiered layers of abstraction that enable a variety of high-level, domain specific languages to be compiled to a common (thin-waist) tasking language; this common tasking language is statically verified and can be subsequently re-translated, if needed, for execution on a wide variety of hardware platforms. snBench provides: (1) a common sensory tasking language (Instruction Set Architecture) powerful enough to express complex SN services, yet simple enough to be executed by highly constrained resources with soft, real-time constraints, (2) a prototype high-level language (and corresponding compiler) to illustrate the utility of the common tasking language and the tiered programming approach in this domain, (3) an execution environment and a run-time support infrastructure that abstract a collection of heterogeneous resources into a single virtual Sensor Network, tasked via this common tasking language, and (4) novel formal methods (i.e., static analysis techniques) that verify safety properties and infer implicit resource constraints to facilitate resource allocation for new services. This thesis presents these components in detail, as well as two specific case-studies: the use of snBench to integrate physical and wireless network security, and the use of snBench as the foundation for semester-long student projects in a graduate-level Software Engineering course

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

BACKGROUND: Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases. RESULTS: We describe the software tools RepbaseSubmitter and Censor, which are designed to facilitate updating and screening the content of Repbase. RepbaseSubmitter is a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position. Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and sensitivity, and can conduct DNA-DNA, DNA-protein, or translated DNA-translated DNA searches of genomic sequence. Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s), repeat sequences found in the query, and alignments. CONCLUSION: Censor and RepbaseSubmitter are available as both web-based services and downloadable versions. They can be found at (RepbaseSubmitter) and (Censor)

The dynamics of Salafism in Pekanbaru : from deprived muslims to a community of memory

This thesis discusses the phenomenon of Islamic revivalism, represented by the Salafi movement in Pekanbaru, Indonesia. It focuses on how this movement tries to solve the problem of existential deprivation among non-religious Muslims by constructing a community of memory in which Salafis share values and beliefs, by referring to the interpretations of their pious predecessors or al-salaf al-sālih. This deprivation is a result of the spread of bid’a and of the perceived negative impacts of modernity. The term al-salaf al-sālih refers to the first three generation of Muslims, while Salafi (pl. Salafis) means the follower of al-salaf al-sālih, and Salafism refers to the interpretations of al-salaf al-sālih. This study addresses questions concerning how the Salafis develop and solve the problem of relative existential deprivation among non-religious Malay Muslims in Pekanbaru. In order to examine this phenomenon, I conducted ethnographic research in Pekanbaru from July 2015 to April 2016, in which I interviewed male Salafis and non-Salafis, and observed and became involved in the Salafi religious and social events. Findings in this study are four-fold. First, derived from relative deprivation theory, I conclude that the return of non-religious Muslims to Islam is as a result of various relative deprivations they have suffered, such as economic, social, and—most significantly—existential deprivation. The second finding is that the return of those deprived Muslims is closely related to cultural position of Islam as an “official” religion of Malay people. In many ways this continues to play a significant role as a key orientating value. The third conclusion is that Salafism is seen as being able to meet the religious and cognitive needs of those new reverts. The former is related to the perception that Salafism is pure, simple and more legitimate compared to other Islamic currents and organisations. The latter, cognitive need, concerns how new reverts search for a way to remove themselves from the prolonged disputes between some Islamic organisations. The fourth conclusion, derived from the theory of memory, is that the Salafi Group can be considered as a community of memory in which all Salafi members maintain a connection to the past (al-salaf al-sālih), guided by the Salafi preachers who serve as the main referents