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Onur Mutlu

Publications and source records attributed to Onur Mutlu.

At least 307 records · Page 17Linked to original sources

A Memory Controller with Row Buffer Locality Awareness for Hybrid Memory Systems

Non-volatile memory (NVM) is a class of promising scalable memory technologies that can potentially offer higher capacity than DRAM at the same cost point. Unfortunately, the access latency and energy of NVM is often higher than those of DRAM, while the endurance of NVM is lower. Many DRAM-NVM hybrid memory systems use DRAM as a cache to NVM, to achieve the low access latency, low energy, and high endurance of DRAM, while taking advantage of the large capacity of NVM. A key question for a hybrid memory system is what data to cache in DRAM to best exploit the advantages of each technology while avoiding the disadvantages of each technology as much as possible. We propose a new memory controller design that improves hybrid memory performance and energy efficiency. We observe that both DRAM and NVM banks employ row buffers that act as a cache for the most recently accessed memory row. Accesses that are row buffer hits incur similar latencies (and energy consumption) in both DRAM and NVM, whereas accesses that are row buffer misses incur longer latencies (and higher energy consumption) in NVM than in DRAM. To exploit this, we devise a policy that caches heavily-reused data that frequently misses in the NVM row buffers into DRAM. Our policy tracks the row buffer miss counts of recently-used rows in NVM, and caches in DRAM the rows that are predicted to incur frequent row buffer misses. Our proposed policy also takes into account the high write latencies of NVM, in addition to row buffer locality and more likely places the write-intensive pages in DRAM instead of NVM.

cs.AR↗

High-Performance and Energy-Effcient Memory Scheduler Design for Heterogeneous Systems

When multiple processor cores (CPUs) and a GPU integrated together on the same chip share the off-chip DRAM, requests from the GPU can heavily interfere with requests from the CPUs, leading to low system performance and starvation of cores. Unfortunately, state-of-the-art memory scheduling algorithms are ineffective at solving this problem due to the very large amount of GPU memory traffic, unless a very large and costly request buffer is employed to provide these algorithms with enough visibility across the global request stream. Previously-proposed memory controller (MC) designs use a single monolithic structure to perform three main tasks. First, the MC attempts to schedule together requests to the same DRAM row to increase row buffer hit rates. Second, the MC arbitrates among the requesters (CPUs and GPU) to optimize for overall system throughput, average response time, fairness and quality of service. Third, the MC manages the low-level DRAM command scheduling to complete requests while ensuring compliance with all DRAM timing and power constraints. This paper proposes a fundamentally new approach, called the Staged Memory Scheduler (SMS), which decouples the three primary MC tasks into three significantly simpler structures that together improve system performance and fairness. Our evaluation shows that SMS provides 41.2% performance improvement and fairness improvement compared to the best previous state-of-the-art technique, while enabling a design that is significantly less complex and more power-efficient to implement.

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Mosaic: An Application-Transparent Hardware-Software Cooperative Memory Manager for GPUs

Modern GPUs face a trade-off on how the page size used for memory management affects address translation and demand paging. Support for multiple page sizes can help relax the page size trade-off so that address translation and demand paging optimizations work together synergistically. However, existing page coalescing and splintering policies require costly base page migrations that undermine the benefits multiple page sizes provide. In this paper, we observe that GPGPU applications present an opportunity to support multiple page sizes without costly data migration, as the applications perform most of their memory allocation en masse (i.e., they allocate a large number of base pages at once). We show that this en masse allocation allows us to create intelligent memory allocation policies which ensure that base pages that are contiguous in virtual memory are allocated to contiguous physical memory pages. As a result, coalescing and splintering operations no longer need to migrate base pages. We introduce Mosaic, a GPU memory manager that provides application-transparent support for multiple page sizes. Mosaic uses base pages to transfer data over the system I/O bus, and allocates physical memory in a way that (1) preserves base page contiguity and (2) ensures that a large page frame contains pages from only a single memory protection domain. This mechanism allows the TLB to use large pages, reducing address translation overhead. During data transfer, this mechanism enables the GPU to transfer only the base pages that are needed by the application over the system I/O bus, keeping demand paging overhead low.

cs.OS↗

Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages, and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we 1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and 2) provide guidelines for determining the appropriate tools for each step. We analyze various combinations of different tools and expose the tradeoffs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, in order to overcome the high error rates of the nanopore sequencing technology.

q-bio.GN↗

Zorua: Enhancing Programming Ease, Portability, and Performance in GPUs by Decoupling Programming Models from Resource Management

The application resource specification--a static specification of several parameters such as the number of threads and the scratchpad memory usage per thread block--forms a critical component of the existing GPU programming models. This specification determines the performance of the application during execution because the corresponding on-chip hardware resources are allocated and managed purely based on this specification. This tight coupling between the software-provided resource specification and resource management in hardware leads to significant challenges in programming ease, portability, and performance, as we demonstrate in this work. Our goal in this work is to reduce the dependence of performance on the software-provided resource specification to simultaneously alleviate the above challenges. To this end, we introduce Zorua, a new resource virtualization framework, that decouples the programmer-specified resource usage of a GPU application from the actual allocation in the on-chip hardware resources. Zorua enables this decoupling by virtualizing each resource transparently to the programmer. We demonstrate that by providing the illusion of more resources than physically available, Zorua offers several important benefits: (i) Programming Ease: Zorua eases the burden on the programmer to provide code that is tuned to efficiently utilize the physically available on-chip resources. (ii) Portability: Zorua alleviates the necessity of re-tuning an application's resource usage when porting the application across GPU generations. (iii) Performance: By dynamically allocating resources and carefully oversubscribing them when necessary, Zorua improves or retains the performance of applications that are already highly tuned to best utilize the resources. The holistic virtualization provided by Zorua has many other potential uses which we describe in this paper.

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Enabling the Adoption of Processing-in-Memory: Challenges, Mechanisms, Future Research Directions

Poor DRAM technology scaling over the course of many years has caused DRAM-based main memory to increasingly become a larger system bottleneck. A major reason for the bottleneck is that data stored within DRAM must be moved across a pin-limited memory channel to the CPU before any computation can take place. This requires a high latency and energy overhead, and the data often cannot benefit from caching in the CPU, making it difficult to amortize the overhead. Modern 3D-stacked DRAM architectures include a logic layer, where compute logic can be integrated underneath multiple layers of DRAM cell arrays within the same chip. Architects can take advantage of the logic layer to perform processing-in-memory (PIM), or near-data processing. In a PIM architecture, the logic layer within DRAM has access to the high internal bandwidth available within 3D-stacked DRAM (which is much greater than the bandwidth available between DRAM and the CPU). Thus, PIM architectures can effectively free up valuable memory channel bandwidth while reducing system energy consumption. A number of important issues arise when we add compute logic to DRAM. In particular, the logic does not have low-latency access to common CPU structures that are essential for modern application execution, such as the virtual memory and cache coherence mechanisms. To ease the widespread adoption of PIM, we ideally would like to maintain traditional virtual memory abstractions and the shared memory programming model. This requires efficient mechanisms that can provide logic in DRAM with access to CPU structures without having to communicate frequently with the CPU. To this end, we propose and evaluate two general-purpose solutions that minimize unnecessary off-chip communication for PIM architectures. We show that both mechanisms improve the performance and energy consumption of many important memory-intensive applications.

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Focus: Querying Large Video Datasets with Low Latency and Low Cost

Large volumes of videos are continuously recorded from cameras deployed for traffic control and surveillance with the goal of answering "after the fact" queries: identify video frames with objects of certain classes (cars, bags) from many days of recorded video. While advancements in convolutional neural networks (CNNs) have enabled answering such queries with high accuracy, they are too expensive and slow. We build Focus, a system for low-latency and low-cost querying on large video datasets. Focus uses cheap ingestion techniques to index the videos by the objects occurring in them. At ingest-time, it uses compression and video-specific specialization of CNNs. Focus handles the lower accuracy of the cheap CNNs by judiciously leveraging expensive CNNs at query-time. To reduce query time latency, we cluster similar objects and hence avoid redundant processing. Using experiments on video streams from traffic, surveillance and news channels, we see that Focus uses 58X fewer GPU cycles than running expensive ingest processors and is 37X faster than processing all the video at query time.

cs.DB↗

Errors in Flash-Memory-Based Solid-State Drives: Analysis, Mitigation, and Recovery

NAND flash memory is ubiquitous in everyday life today because its capacity has continuously increased and cost has continuously decreased over decades. This positive growth is a result of two key trends: (1) effective process technology scaling; and (2) multi-level (e.g., MLC, TLC) cell data coding. Unfortunately, the reliability of raw data stored in flash memory has also continued to become more difficult to ensure, because these two trends lead to (1) fewer electrons in the flash memory cell floating gate to represent the data; and (2) larger cell-to-cell interference and disturbance effects. Without mitigation, worsening reliability can reduce the lifetime of NAND flash memory. As a result, flash memory controllers in solid-state drives (SSDs) have become much more sophisticated: they incorporate many effective techniques to ensure the correct interpretation of noisy data stored in flash memory cells. In this chapter, we review recent advances in SSD error characterization, mitigation, and data recovery techniques for reliability and lifetime improvement. We provide rigorous experimental data from state-of-the-art MLC and TLC NAND flash devices on various types of flash memory errors, to motivate the need for such techniques. Based on the understanding developed by the experimental characterization, we describe several mitigation and recovery techniques, including (1) cell-tocell interference mitigation; (2) optimal multi-level cell sensing; (3) error correction using state-of-the-art algorithms and methods; and (4) data recovery when error correction fails. We quantify the reliability improvement provided by each of these techniques. Looking forward, we briefly discuss how flash memory and these techniques could evolve into the future.

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Improving DRAM Performance by Parallelizing Refreshes with Accesses

Modern DRAM cells are periodically refreshed to prevent data loss due to leakage. Commodity DDR DRAM refreshes cells at the rank level. This degrades performance significantly because it prevents an entire rank from serving memory requests while being refreshed. DRAM designed for mobile platforms, LPDDR DRAM, supports an enhanced mode, called per-bank refresh, that refreshes cells at the bank level. This enables a bank to be accessed while another in the same rank is being refreshed, alleviating part of the negative performance impact of refreshes. However, there are two shortcomings of per-bank refresh. First, the per-bank refresh scheduling scheme does not exploit the full potential of overlapping refreshes with accesses across banks because it restricts the banks to be refreshed in a sequential round-robin order. Second, accesses to a bank that is being refreshed have to wait. To mitigate the negative performance impact of DRAM refresh, we propose two complementary mechanisms, DARP (Dynamic Access Refresh Parallelization) and SARP (Subarray Access Refresh Parallelization). The goal is to address the drawbacks of per-bank refresh by building more efficient techniques to parallelize refreshes and accesses within DRAM. First, instead of issuing per-bank refreshes in a round-robin order, DARP issues per-bank refreshes to idle banks in an out-of-order manner. Furthermore, DARP schedules refreshes during intervals when a batch of writes are draining to DRAM. Second, SARP exploits the existence of mostly-independent subarrays within a bank. With minor modifications to DRAM organization, it allows a bank to serve memory accesses to an idle subarray while another subarray is being refreshed. Extensive evaluations show that our mechanisms improve system performance and energy efficiency compared to state-of-the-art refresh policies and the benefit increases as DRAM density increases.

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GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies

Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read mappers 1) quickly generate possible mapping locations for seeds (i.e., smaller segments) within each read, 2) extract reference sequences at each of the mapping locations, and 3) check similarity between each read and its associated reference sequences with a computationally-expensive algorithm (i.e., sequence alignment) to determine the origin of the read. A seed location filter comes into play before alignment, discarding seed locations that alignment would deem a poor match. The ideal seed location filter would discard all poor match locations prior to alignment such that there is no wasted computation on unnecessary alignments. Results: We propose a novel seed location filtering algorithm, GRIM-Filter, optimized to exploit 3D-stacked memory systems that integrate computation within a logic layer stacked under memory layers, to perform processing-in-memory (PIM). GRIM-Filter quickly filters seed locations by 1) introducing a new representation of coarse-grained segments of the reference genome, and 2) using massively-parallel in-memory operations to identify read presence within each coarse-grained segment. Our evaluations show that for a sequence alignment error tolerance of 0.05, GRIM-Filter 1) reduces the false negative rate of filtering by 5.59x--6.41x, and 2) provides an end-to-end read mapper speedup of 1.81x--3.65x, compared to a state-of-the-art read mapper employing the best previous seed location filtering algorithm. Availability: The code is available online at: https://github.com/CMU-SAFARI/GRIM

q-bio.GN↗

Error Characterization, Mitigation, and Recovery in Flash Memory Based Solid-State Drives

NAND flash memory is ubiquitous in everyday life today because its capacity has continuously increased and cost has continuously decreased over decades. This positive growth is a result of two key trends: (1) effective process technology scaling, and (2) multi-level (e.g., MLC, TLC) cell data coding. Unfortunately, the reliability of raw data stored in flash memory has also continued to become more difficult to ensure, because these two trends lead to (1) fewer electrons in the flash memory cell (floating gate) to represent the data and (2) larger cell-to-cell interference and disturbance effects. Without mitigation, worsening reliability can reduce the lifetime of NAND flash memory. As a result, flash memory controllers in solid-state drives (SSDs) have become much more sophisticated: they incorporate many effective techniques to ensure the correct interpretation of noisy data stored in flash memory cells. In this article, we review recent advances in SSD error characterization, mitigation, and data recovery techniques for reliability and lifetime improvement. We provide rigorous experimental data from state-of-the-art MLC and TLC NAND flash devices on various types of flash memory errors, to motivate the need for such techniques. Based on the understanding developed by the experimental characterization, we describe several mitigation and recovery techniques, including (1) cell-to-cell interference mitigation, (2) optimal multi-level cell sensing, (3) error correction using state-of-the-art algorithms and methods, and (4) data recovery when error correction fails. We quantify the reliability improvement provided by each of these techniques. Looking forward, we briefly discuss how flash memory and these techniques could evolve into the future.

cs.AR↗

Improving Multi-Application Concurrency Support Within the GPU Memory System

GPUs exploit a high degree of thread-level parallelism to hide long-latency stalls. Due to the heterogeneous compute requirements of different applications, there is a growing need to share the GPU across multiple applications in large-scale computing environments. However, while CPUs offer relatively seamless multi-application concurrency, and are an excellent fit for multitasking and for virtualized environments, GPUs currently offer only primitive support for multi-application concurrency. Much of the problem in a contemporary GPU lies within the memory system, where multi-application execution requires virtual memory support to manage the address spaces of each application and to provide memory protection. In this work, we perform a detailed analysis of the major problems in state-of-the-art GPU virtual memory management that hinders multi-application execution. Existing GPUs are designed to share memory between the CPU and GPU, but do not handle multi-application support within the GPU well. We find that when multiple applications spatially share the GPU, there is a significant amount of inter-core thrashing on the shared TLB within the GPU. The TLB contention is high enough to prevent the GPU from successfully hiding stall latencies, thus becoming a first-order performance concern. We introduce MASK, a memory hierarchy design that provides low-overhead virtual memory support for the concurrent execution of multiple applications. MASK extends the GPU memory hierarchy to efficiently support address translation through the use of multi-level TLBs, and uses translation-aware memory and cache management to maximize throughput in the presence of inter-application contention.

cs.AR↗

GRIM-filter: fast seed filtering in read mapping using emerging memory technologies

Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly generate possible mapping locations (i.e., seeds) for each read, 2) extract reference sequences at each of the mapping locations, and then 3) check similarity between each read and its associated reference sequences with a computationally expensive dynamic programming algorithm (alignment) to determine the origin of the read. Location filters come into play before alignment, discarding seed locations that alignment would have deemed a poor match. The ideal location filter would discard all poor matching locations prior to alignment such that there is no wasted computation on poor alignments. Results: We propose a novel filtering algorithm, GRIM-Filter, optimized to exploit emerging 3D-stacked memory systems that integrate computation within a stacked logic layer, enabling processing-in-memory (PIM). GRIM-Filter quickly filters locations by 1) introducing a new representation of coarse-grained segments of the reference genome and 2) using massively-parallel in-memory operations to identify read presence within each coarse-grained segment. Our evaluations show that for 5% error acceptance rates, GRIM-Filter eliminates 5.59x-6.41x more false negatives and exhibits end-to-end speedups of 1.81x-3.65x compared to mappers employing the best previous filtering algorithm.

q-bio.GN↗

MAGNET: Understanding and Improving the Accuracy of Genome Pre-Alignment Filtering

In the era of high throughput DNA sequencing (HTS) technologies, calculating the edit distance (i.e., the minimum number of substitutions, insertions, and deletions between a pair of sequences) for billions of genomic sequences is the computational bottleneck in todays read mappers. The shifted Hamming distance (SHD) algorithm proposes a fast filtering strategy that can rapidly filter out invalid mappings that have more edits than allowed. However, SHD shows high inaccuracy in its filtering by admitting invalid mappings to be marked as correct ones. This wastes the execution time and imposes a large computational burden. In this work, we comprehensively investigate four sources that lead to the filtering inaccuracy. We propose MAGNET, a new filtering strategy that maintains high accuracy across different edit distance thresholds and data sets. It significantly improves the accuracy of pre-alignment filtering by one to two orders of magnitude. The MATLAB implementations of MAGNET and SHD are open source and available at: https://github.com/BilkentCompGen/MAGNET.

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Using ECC DRAM to Adaptively Increase Memory Capacity

Modern DRAM modules are often equipped with hardware error correction capabilities, especially for DRAM deployed in large-scale data centers, as process technology scaling has increased the susceptibility of these devices to errors. To provide fast error detection and correction, error-correcting codes (ECC) are placed on an additional DRAM chip in a DRAM module. This additional chip expands the raw capacity of a DRAM module by 12.5%, but the applications are unable to use any of this extra capacity, as it is used exclusively to provide reliability for all data. In reality, there are a number of applications that do not need such strong reliability for all their data regions (e.g., some user batch jobs executing on a public cloud), and can instead benefit from using additional DRAM capacity to store extra data. Our goal in this work is to provide the additional capacity within an ECC DRAM module to applications when they do not need the high reliability of error correction. In this paper, we propose Capacity- and Reliability-Adaptive Memory (CREAM), a hardware mechanism that adapts error correcting DRAM modules to offer multiple levels of error protection, and provides the capacity saved from using weaker protection to applications. For regions of memory that do not require strong error correction, we either provide no ECC protection or provide error detection using multibit parity. We evaluate several layouts for arranging the data within ECC DRAM in these reduced-protection modes, taking into account the various trade-offs exposed from exploiting the extra chip. Our experiments show that the increased capacity provided by CREAM improves performance by 23.0% for a memory caching workload, and by 37.3% for a commercial web search workload executing production query traces. In addition, CREAM can increase bank-level parallelism within DRAM, offering further performance improvements.

cs.AR↗

LazyPIM: Efficient Support for Cache Coherence in Processing-in-Memory Architectures

Processing-in-memory (PIM) architectures have seen an increase in popularity recently, as the high internal bandwidth available within 3D-stacked memory provides greater incentive to move some computation into the logic layer of the memory. To maintain program correctness, the portions of a program that are executed in memory must remain coherent with the portions of the program that continue to execute within the processor. Unfortunately, PIM architectures cannot use traditional approaches to cache coherence due to the high off-chip traffic consumed by coherence messages, which, as we illustrate in this work, can undo the benefits of PIM execution for many data-intensive applications. We propose LazyPIM, a new hardware cache coherence mechanism designed specifically for PIM. Prior approaches for coherence in PIM are ill-suited to applications that share a large amount of data between the processor and the PIM logic. LazyPIM uses a combination of speculative cache coherence and compressed coherence signatures to greatly reduce the overhead of keeping PIM coherent with the processor, even when a large amount of sharing exists.We find that LazyPIM improves average performance across a range of data-intensive PIM applications by 19.6%, reduces off-chip traffic by 30.9%, and reduces energy consumption by 18.0%, over the best prior approaches to PIM coherence.

cs.AR↗

Understanding Reduced-Voltage Operation in Modern DRAM Chips: Characterization, Analysis, and Mechanisms

The energy consumption of DRAM is a critical concern in modern computing systems. Improvements in manufacturing process technology have allowed DRAM vendors to lower the DRAM supply voltage conservatively, which reduces some of the DRAM energy consumption. We would like to reduce the DRAM supply voltage more aggressively, to further reduce energy. Aggressive supply voltage reduction requires a thorough understanding of the effect voltage scaling has on DRAM access latency and DRAM reliability. In this paper, we take a comprehensive approach to understanding and exploiting the latency and reliability characteristics of modern DRAM when the supply voltage is lowered below the nominal voltage level specified by DRAM standards. Using an FPGA-based testing platform, we perform an experimental study of 124 real DDR3L (low-voltage) DRAM chips manufactured recently by three major DRAM vendors. We find that reducing the supply voltage below a certain point introduces bit errors in the data, and we comprehensively characterize the behavior of these errors. We discover that these errors can be avoided by increasing the latency of three major DRAM operations (activation, restoration, and precharge). We perform detailed DRAM circuit simulations to validate and explain our experimental findings. We also characterize the various relationships between reduced supply voltage and error locations, stored data patterns, DRAM temperature, and data retention. Based on our observations, we propose a new DRAM energy reduction mechanism, called Voltron. The key idea of Voltron is to use a performance model to determine by how much we can reduce the supply voltage without introducing errors and without exceeding a user-specified threshold for performance loss. Voltron reduces the average system energy by 7.3% while limiting the average system performance loss to only 1.8%, for a variety of workloads.

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Understanding and Exploiting Design-Induced Latency Variation in Modern DRAM Chips

Variation has been shown to exist across the cells within a modern DRAM chip. We empirically demonstrate a new form of variation that exists within a real DRAM chip, induced by the design and placement of different components in the DRAM chip. Our goals are to understand design-induced variation that exists in real, state-of-the-art DRAM chips, exploit it to develop low-cost mechanisms that can dynamically find and use the lowest latency at which to operate a DRAM chip reliably, and, thus, improve overall system performance while ensuring reliable system operation. To this end, we first experimentally demonstrate and analyze designed-induced variation in modern DRAM devices by testing and characterizing 96 DIMMs (768 DRAM chips). Our characterization identifies DRAM regions that are vulnerable to errors, if operated at lower latency, and finds consistency in their locations across a given DRAM chip generation, due to design-induced variation. Based on our extensive experimental analysis, we develop two mechanisms that reliably reduce DRAM latency. First, DIVA Profiling uses runtime profiling to dynamically identify the lowest DRAM latency that does not introduce failures. DIVA Profiling exploits design-induced variation and periodically profiles only the vulnerable regions to determine the lowest DRAM latency at low cost. Our second mechanism, DIVA Shuffling, shuffles data such that values stored in vulnerable regions are mapped to multiple error-correcting code (ECC) codewords. Combined together, our two mechanisms reduce read/write latency by 40.0%/60.5%, which translates to an overall system performance improvement of 14.7%/13.7%/13.8% (in 2-/4-/8-core systems) across a variety of workloads, while ensuring reliable operation.

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