arXiv subjects

Onur Mutlu

Publications and source records attributed to Onur Mutlu.

At least 55 records · Page 3Linked to original sources

arXiv2026

ALPHA-PIM: Analysis of Linear Algebraic Processing for High-Performance Graph Applications on a Real Processing-In-Memory System

Processing large-scale graph datasets is computationally intensive and time-consuming. Processor-centric CPU and GPU architectures, commonly used for graph applications, often face bottlenecks caused by extensive data movement between the processor and memory units due to low data reuse. As a result, these applications are often memory-bound, limiting both performance and energy efficiency due to excessive data transfers. Processing-In-Memory (PIM) offers a promising approach to mitigate data movement bottlenecks by integrating computation directly within or near memory. Although several previous studies have introduced custom PIM proposals for graph processing, they do not leverage real-world PIM systems. This work aims to explore the capabilities and characteristics of common graph algorithms on a real-world PIM system to accelerate data-intensive graph workloads. To this end, we (1) implement representative graph algorithms on UPMEM's general-purpose PIM architecture; (2) characterize their performance and identify key bottlenecks; (3) compare results against CPU and GPU baselines; and (4) derive insights to guide future PIM hardware design. Our study underscores the importance of selecting optimal data partitioning strategies across PIM cores to maximize performance. Additionally, we identify critical hardware limitations in current PIM architectures and emphasize the need for future enhancements across computation, memory, and communication subsystems. Key opportunities for improvement include increasing instruction-level parallelism, developing improved DMA engines with non-blocking capabilities, and enabling direct interconnection networks among PIM cores to reduce data transfer overheads.

cs.DC↗

arXiv2026

Processing-in-memory for genomics workloads

Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data are currently processed in energy-hungry computer clusters and centers, necessitating data transfer, consuming substantial energy, and wasting valuable time. Therefore, there is a need for fast, energy-efficient, and cost-efficient technologies that enable genomics research without requiring data centers and cloud platforms. We recently launched the BioPIM Project to leverage emerging processing-in-memory (PIM) technologies to enable energy- and cost-efficient analysis of bioinformatics workloads. The BioPIM Project focuses on co-designing algorithms and data structures commonly used in genomics with several PIM architectures to achieve the highest cost, energy, and time savings.

q-bio.GN↗

arXiv2026

GenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read Mapping

Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a reference genome. Read mapping for short reads comes in two forms: single-end and paired-end, with the latter being more prevalent due to its higher accuracy and support for advanced analysis. Read mapping remains a major performance bottleneck in genome analysis due to expensive dynamic programming. Prior efforts have attempted to mitigate this cost by employing filters to identify and potentially discard computationally expensive matches and leveraging hardware accelerators to speed up the computations. While partially effective, these approaches have limitations. In particular, existing filters are often ineffective for paired-end reads, as they evaluate each read independently and exhibit relatively low filtering ratios. In this work, we propose GenPairX, a hardware-algorithm co-designed accelerator that efficiently minimizes the computational load of paired-end read mapping while enhancing the throughput of memory-intensive operations. GenPairX introduces: (1) a novel filtering algorithm that jointly considers both reads in a pair to improve filtering effectiveness, and a lightweight alignment algorithm to replace most of the computationally expensive dynamic programming operations, and (2) two specialized hardware mechanisms to support the proposed algorithms. Our evaluations show that GenPairX delivers substantial performance improvements over state-of-the-art solutions, achieving 1575x and 1.43x higher throughput per watt compared to leading CPU-based and accelerator-based read mappers, respectively, all without compromising accuracy.

cs.AR↗

arXiv2026

Athena: Synergizing Data Prefetching and Off-Chip Prediction via Online Reinforcement Learning

Prefetching and off-chip prediction are two techniques proposed to hide long memory access latencies in high-performance processors. In this work, we demonstrate that: (1) prefetching and off-chip prediction often provide complementary performance benefits, yet (2) naively combining them often fails to realize their full performance potential, and (3) existing prefetcher control policies leave significant room for performance improvement behind. Our goal is to design a holistic framework that can autonomously learn to coordinate an off-chip predictor with multiple prefetchers employed at various cache levels. To this end, we propose a new technique called Athena, which models the coordination between prefetchers and off-chip predictor (OCP) as a reinforcement learning (RL) problem. Athena acts as the RL agent that observes multiple system-level features (e.g., prefetcher/OCP accuracy, bandwidth usage) over an epoch of program execution, and uses them as state information to select a coordination action (i.e., enabling the prefetcher and/or OCP, and adjusting prefetcher aggressiveness). At the end of every epoch, Athena receives a numerical reward that measures the change in multiple system-level metrics (e.g., number of cycles taken to execute an epoch). Athena uses this reward to autonomously and continuously learn a policy to coordinate prefetchers with OCP. Our extensive evaluation using a diverse set of memory-intensive workloads shows that Athena consistently outperforms prior state-of-the-art coordination policies across a wide range of system configurations with various combinations of underlying prefetchers, OCPs, and main memory bandwidths, while incurring only modest storage overhead. Athena is freely available at https://github.com/CMU-SAFARI/Athena.

cs.AR↗

arXiv2026

Conduit: Programmer-Transparent Near-Data Processing Using Multiple Compute-Capable Resources in Solid State Drives

Solid-state drives (SSDs) are well suited for near-data processing (NDP) because they: (1) store large application datasets, and (2) support three NDP paradigms: in-storage processing (ISP), processing using DRAM in the SSD (PuD-SSD), and in-flash processing (IFP). A large body of prior SSD-based NDP techniques operate in isolation, mapping computations to only one or two NDP paradigms (i.e., ISP, PuD-SSD, or IFP) within the SSD. These techniques (1) are tailored to specific workloads or kernels, (2) do not exploit the full computational potential of an SSD, and (3) lack programmer-transparency. While several prior works propose techniques to partition computation between the host and near-memory accelerators, adapting these techniques to SSDs has limited benefits because they (1) ignore the heterogeneity of the SSD resources, and (2) make offloading decisions based on limited factors such as bandwidth utilization, or data movement cost. We propose Conduit, a general-purpose, programmer-transparent NDP framework for SSDs that leverages multiple SSD computation resources. At compile time, Conduit executes a custom compiler (e.g., LLVM) pass that (i) vectorizes suitable application code segments into SIMD operations that align with the SSD's page layout, and (ii) embeds metadata (e.g., operation type, operand sizes) into the vectorized instructions to guide runtime offloading decisions. At runtime, within the SSD, Conduit performs instruction-granularity offloading by evaluating six key features, and uses a cost function to select the most suitable SSD resource. We evaluate Conduit and two prior NDP offloading techniques using an in-house event-driven SSD simulator on six data-intensive workloads. Conduit outperforms the best-performing prior offloading policy by 1.8x and reduces energy consumption by 46%.

cs.AR↗

arXiv2026

SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Sequence Analysis

Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are extensive efforts to accelerate genome sequence analysis. In this work, we demonstrate a major bottleneck that greatly limits and diminishes the benefits of state-of-the-art genome sequence analysis accelerators: the data preparation bottleneck, where genomic sequence data is stored in compressed form and needs to be first decompressed and formatted before an accelerator can operate on it. To mitigate this bottleneck, we propose SAGe, an algorithm-architecture co-design for highly-compressed storage and high-performance access of large-scale genomic sequence data. The key challenge is to improve data preparation performance while maintaining high compression ratios (comparable to genomic-specific compression algorithms) at low hardware cost. We address this challenge by leveraging key properties of genomic datasets to co-design (i) a lossless (de)compression algorithm, (ii) hardware that decompresses data with lightweight operations and efficient streaming accesses, (iii) storage data layout, and (iv) interface commands to access data. SAGe is highly versatile, as it supports datasets from different sequencing technologies and species. Due to its lightweight design, SAGe can be seamlessly integrated with a broad range of hardware accelerators for genome sequence analysis to mitigate their data preparation bottlenecks. Our results demonstrate that SAGe improves the average end-to-end performance and energy efficiency of two state-of-the-art genome sequence analysis accelerators by 3.0x-32.1x and 13.0x-34.0x, respectively, compared to when the accelerators rely on state-of-the-art software and hardware decompression tools.

cs.AR↗

arXiv2025

REIS: A High-Performance and Energy-Efficient Retrieval System with In-Storage Processing

Large Language Models (LLMs) face an inherent challenge: their knowledge is confined to the data that they have been trained on. To overcome this issue, Retrieval-Augmented Generation (RAG) complements the static training-derived knowledge of LLMs with an external knowledge repository. RAG consists of three stages: indexing, retrieval, and generation. The retrieval stage of RAG becomes a significant bottleneck in inference pipelines. In this stage, a user query is mapped to an embedding vector and an Approximate Nearest Neighbor Search (ANNS) algorithm searches for similar vectors in the database to identify relevant items. Due to the large database sizes, ANNS incurs significant data movement overheads between the host and the storage system. To alleviate these overheads, prior works propose In-Storage Processing (ISP) techniques that accelerate ANNS by performing computations inside storage. However, existing works that leverage ISP for ANNS (i) employ algorithms that are not tailored to ISP systems, (ii) do not accelerate data retrieval operations for data selected by ANNS, and (iii) introduce significant hardware modifications, limiting performance and hindering their adoption. We propose REIS, the first ISP system tailored for RAG that addresses these limitations with three key mechanisms. First, REIS employs a database layout that links database embedding vectors to their associated documents, enabling efficient retrieval. Second, it enables efficient ANNS by introducing an ISP-tailored data placement technique that distributes embeddings across the planes of the storage system and employs a lightweight Flash Translation Layer. Third, REIS leverages an ANNS engine that uses the existing computational resources inside the storage system. Compared to a server-grade system, REIS improves the performance (energy efficiency) of retrieval by an average of 13x (55x).

cs.CL↗

arXiv2025

In-DRAM True Random Number Generation Using Simultaneous Multiple-Row Activation: An Experimental Study of Real DRAM Chips

In this work, we experimentally demonstrate that it is possible to generate true random numbers at high throughput and low latency in commercial off-the-shelf (COTS) DRAM chips by leveraging simultaneous multiple-row activation (SiMRA) via an extensive characterization of 96 DDR4 DRAM chips. We rigorously analyze SiMRA's true random generation potential in terms of entropy, latency, and throughput for varying numbers of simultaneously activated DRAM rows (i.e., 2, 4, 8, 16, and 32), data patterns, temperature levels, and spatial variations. Among our 11 key experimental observations, we highlight four key results. First, we evaluate the quality of our TRNG designs using the commonly-used NIST statistical test suite for randomness and find that all SiMRA-based TRNG designs successfully pass each test. Second, 2-, 8-, 16-, and 32-row activation-based TRNG designs outperform the state-of-theart DRAM-based TRNG in throughput by up to 1.15x, 1.99x, 1.82x, and 1.39x, respectively. Third, SiMRA's entropy tends to increase with the number of simultaneously activated DRAM rows. Fourth, operational parameters and conditions (e.g., data pattern and temperature) significantly affect entropy. For example, for most of the tested modules, the average entropy of 32-row activation is 2.51x higher than that of 2-row activation. For example, increasing the temperature from 50°C to 90°C decreases SiMRA's entropy by 1.53x for 32-row activation. To aid future research and development, we open-source our infrastructure at https://github.com/CMU-SAFARI/SiMRA-TRNG.

cs.AR↗

arXiv2025

DRAM Bender: An Extensible and Versatile FPGA-based Infrastructure to Easily Test State-of-the-art DRAM Chips

To understand and improve DRAM performance, reliability, security and energy efficiency, prior works study characteristics of commodity DRAM chips. Unfortunately, state-of-the-art open source infrastructures capable of conducting such studies are obsolete, poorly supported, or difficult to use, or their inflexibility limit the types of studies they can conduct. We propose DRAM Bender, a new FPGA-based infrastructure that enables experimental studies on state-of-the-art DRAM chips. DRAM Bender offers three key features at the same time. First, DRAM Bender enables directly interfacing with a DRAM chip through its low-level interface. This allows users to issue DRAM commands in arbitrary order and with finer-grained time intervals compared to other open source infrastructures. Second, DRAM Bender exposes easy-to-use C++ and Python programming interfaces, allowing users to quickly and easily develop different types of DRAM experiments. Third, DRAM Bender is easily extensible. The modular design of DRAM Bender allows extending it to (i) support existing and emerging DRAM interfaces, and (ii) run on new commercial or custom FPGA boards with little effort. To demonstrate that DRAM Bender is a versatile infrastructure, we conduct three case studies, two of which lead to new observations about the DRAM RowHammer vulnerability. In particular, we show that data patterns supported by DRAM Bender uncovers a larger set of bit-flips on a victim row compared to the data patterns commonly used by prior work. We demonstrate the extensibility of DRAM Bender by implementing it on five different FPGAs with DDR4 and DDR3 support. DRAM Bender is freely and openly available at https://github.com/CMU-SAFARI/DRAM-Bender.

cs.AR↗

arXiv2025

ColumnDisturb: Understanding Column-based Read Disturbance in Real DRAM Chips and Implications for Future Systems

We experimentally demonstrate a new widespread read disturbance phenomenon, ColumnDisturb, in real commodity DRAM chips. By repeatedly opening or keeping a DRAM row (aggressor row) open, we show that it is possible to disturb DRAM cells through a DRAM column (i.e., bitline) and induce bitflips in DRAM cells sharing the same columns as the aggressor row (across multiple DRAM subarrays). With ColumnDisturb, the activation of a single row concurrently disturbs cells across as many as three subarrays (e.g., 3072 rows) as opposed to RowHammer/RowPress, which affect only a few neighboring rows of the aggressor row in a single subarray. We rigorously characterize ColumnDisturb and its characteristics under various operational conditions using 216 DDR4 and 4 HBM2 chips from three major manufacturers. Among our 27 key experimental observations, we highlight two major results and their implications. First, ColumnDisturb affects chips from all three major manufacturers and worsens as DRAM technology scales down to smaller node sizes (e.g., the minimum time to induce the first ColumnDisturb bitflip reduces by up to 5.06x). We observe that, in existing DRAM chips, ColumnDisturb induces bitflips within a standard DDR4 refresh window (e.g., in 63.6 ms) in multiple cells. We predict that, as DRAM technology node size reduces, ColumnDisturb would worsen in future DRAM chips, likely causing many more bitflips in the standard refresh window. Second, ColumnDisturb induces bitflips in many (up to 198x) more rows than retention failures. Therefore, ColumnDisturb has strong implications for retention-aware refresh mechanisms that leverage the heterogeneity in cell retention times: our detailed analyses show that ColumnDisturb greatly reduces the benefits of such mechanisms.

cs.AR↗

arXiv2025

Understanding and Mitigating Covert Channel and Side Channel Vulnerabilities Introduced by RowHammer Defenses

DRAM chips are vulnerable to read disturbance phenomena (e.g., RowHammer and RowPress), where repeatedly accessing or keeping open a DRAM row causes bitflips in nearby rows. Attackers leverage RowHammer bitflips in real systems to take over systems and leak data. Consequently, many prior works propose defenses, including recent DDR specifications introducing new defenses (e.g., PRAC and RFM). For robust operation, it is critical to analyze other security implications of RowHammer defenses. Unfortunately, no prior work analyzes the timing covert and side channel vulnerabilities introduced by RowHammer defenses. This paper presents the first analysis and evaluation of timing covert and side channel vulnerabilities introduced by state-of-the-art RowHammer defenses. We demonstrate that RowHammer defenses' preventive actions have two fundamental features that enable timing channels. First, preventive actions reduce DRAM bandwidth availability, resulting in longer memory latencies. Second, preventive actions can be triggered on demand depending on memory access patterns. We introduce LeakyHammer, a new class of attacks that leverage the RowHammer defense-induced memory latency differences to establish communication channels and leak secrets. First, we build two covert channel attacks exploiting two state-of-the-art RowHammer defenses, achieving 39.0 Kbps and 48.7 Kbps channel capacity. Second, we demonstrate a website fingerprinting attack that identifies visited websites based on the RowHammer-preventive actions they cause. We propose and evaluate three countermeasures against LeakyHammer. Our results show that fundamentally mitigating LeakyHammer induces large performance overheads in highly RowHammer-vulnerable systems. We believe and hope our work can enable and aid future work on designing better solutions and more robust systems in the presence of such new vulnerabilities.

cs.CR↗

arXiv2025

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques

Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to millions of bases in a single read), and the option to selectively stop sequencing a molecule before completion. Traditionally, the raw electrical signals generated during sequencing are converted into DNA sequences through a process called basecalling, which typically relies on large neural network models. Raw signal analysis has emerged as a promising alternative to these resource-intensive approaches. While attempts have been made to benchmark conventional basecalling methods, existing evaluation frameworks 1) overlook raw signal analysis techniques, 2) lack the flexibility to accommodate new raw signal analysis tools easily, and 3) fail to include the latest improvements in nanopore datasets. Our goal is to provide an extensible benchmarking framework that enables designing and comparing new methods for raw signal analysis. To this end, we introduce RawBench, the first flexible framework for evaluating raw nanopore signal analysis techniques. RawBench provides modular evaluation of three core pipeline components: 1) reference genome encoding (using different pore models), 2) signal encoding (through various segmentation methods), and 3) representation matching (via different data structures). We extensively evaluate raw signal analysis techniques in terms of 1) quality and performance for read mapping, 2) quality and performance for read classification, and 3) quality of raw signal analysis-assisted basecalling. Our evaluations show that raw signal analysis can achieve competitive quality while significantly reducing resource requirements, particularly in settings where real-time processing or edge deployment is necessary.

q-bio.GN↗

arXiv2025

TeraAgent: A Distributed Agent-Based Simulation Engine for Simulating Half a Trillion Agents

Agent-based simulation is an indispensable paradigm for studying complex systems. These systems can comprise billions of agents, requiring the computing resources of multiple servers to simulate. Unfortunately, the state-of-the-art platform, BioDynaMo, does not scale out across servers due to its shared-memory-based implementation. To overcome this key limitation, we introduce TeraAgent, a distributed agent-based simulation engine. A critical challenge in distributed execution is the exchange of agent information across servers, which we identify as a major performance bottleneck. We propose two solutions: 1) a tailored serialization mechanism that allows agents to be accessed and mutated directly from the receive buffer, and 2) leveraging the iterative nature of agent-based simulations to reduce data transfer with delta encoding. Built on our solutions, TeraAgent enables extreme-scale simulations with half a trillion agents (an 84x improvement), reduces time-to-result with additional compute nodes, improves interoperability with third-party tools, and provides users with more hardware flexibility.

cs.DC↗

arXiv2025

A decentralized future for the open-science databases

Continuous and reliable access to curated biological data repositories is indispensable for accelerating rigorous scientific inquiry and fostering reproducible research. Centralized repositories, though widely used, are vulnerable to single points of failure arising from cyberattacks, technical faults, natural disasters, or funding and political uncertainties. This can lead to widespread data unavailability, data loss, integrity compromises, and substantial delays in critical research, ultimately impeding scientific progress. Centralizing essential scientific resources in a single geopolitical or institutional hub is inherently dangerous, as any disruption can paralyze diverse ongoing research. The rapid acceleration of data generation, combined with an increasingly volatile global landscape, necessitates a critical re-evaluation of the sustainability of centralized models. Implementing federated and decentralized architectures presents a compelling and future-oriented pathway to substantially strengthen the resilience of scientific data infrastructures, thereby mitigating vulnerabilities and ensuring the long-term integrity of data. Here, we examine the structural limitations of centralized repositories, evaluate federated and decentralized models, and propose a hybrid framework for resilient, FAIR, and sustainable scientific data stewardship. Such an approach offers a significant reduction in exposure to governance instability, infrastructural fragility, and funding volatility, and also fosters fairness and global accessibility. The future of open science depends on integrating these complementary approaches to establish a globally distributed, economically sustainable, and institutionally robust infrastructure that safeguards scientific data as a public good, further ensuring continued accessibility, interoperability, and preservation for generations to come.

cs.DB↗

arXiv2025

Chronus: Understanding and Securing the Cutting-Edge Industry Solutions to DRAM Read Disturbance

We 1) present the first rigorous security, performance, energy, and cost analyses of the state-of-the-art on-DRAM-die read disturbance mitigation method, Per Row Activation Counting (PRAC) and 2) propose Chronus, a new mechanism that addresses PRAC's two major weaknesses. Our analysis shows that PRAC's system performance overhead on benign applications is non-negligible for modern DRAM chips and prohibitively large for future DRAM chips that are more vulnerable to read disturbance. We identify two weaknesses of PRAC that cause these overheads. First, PRAC increases critical DRAM access latency parameters due to the additional time required to increment activation counters. Second, PRAC performs a constant number of preventive refreshes at a time, making it vulnerable to an adversarial access pattern, known as the wave attack, and consequently requiring it to be configured for significantly smaller activation thresholds. To address PRAC's two weaknesses, we propose a new on-DRAM-die RowHammer mitigation mechanism, Chronus. Chronus 1) updates row activation counters concurrently while serving accesses by separating counters from the data and 2) prevents the wave attack by dynamically controlling the number of preventive refreshes performed. Our performance analysis shows that Chronus's system performance overhead is near-zero for modern DRAM chips and very low for future DRAM chips. Chronus outperforms three variants of PRAC and three other state-of-the-art read disturbance solutions. We discuss Chronus's and PRAC's implications for future systems and foreshadow future research directions. To aid future research, we open-source our Chronus implementation at https://github.com/CMU-SAFARI/Chronus.

cs.CR↗

arXiv2025

Memory-Centric Computing: Solving Computing's Memory Problem

Computing has a huge memory problem. The memory system, consisting of multiple technologies at different levels, is responsible for most of the energy consumption, performance bottlenecks, robustness problems, monetary cost, and hardware real estate of a modern computing system. All this becomes worse as modern and emerging applications become more data-intensive (as we readily witness in e.g., machine learning, genome analysis, graph processing, and data analytics), making the memory system an even larger bottleneck. In this paper, we discuss two major challenges that greatly affect computing system performance and efficiency: 1) memory technology & capacity scaling (at the lower device and circuit levels) and 2) system and application performance & energy scaling (at the higher levels of the computing stack). We demonstrate that both types of scaling have become extremely difficult, wasteful, and costly due to the dominant processor-centric design & execution paradigm of computers, which treats memory as a dumb and inactive component that cannot perform any computation. We show that moving to a memory-centric design & execution paradigm can solve the major challenges, while enabling multiple other potential benefits. In particular, we demonstrate that: 1) memory technology scaling problems (e.g., RowHammer, RowPress, Variable Read Disturbance, data retention, and other issues awaiting to be discovered) can be much more easily and efficiently handled by enabling memory to autonomously manage itself; 2) system and application performance & energy efficiency can, at the same time, be improved by orders of magnitude by enabling computation capability in memory chips and structures (i.e., processing in memory). We discuss adoption challenges against enabling memory-centric computing, and describe how we can get there step-by-step via an evolutionary path.

cs.AR↗

arXiv2025

Self-Managing DRAM: A Low-Cost Framework for Enabling Autonomous and Efficient in-DRAM Operations

The memory controller is in charge of managing DRAM maintenance operations (e.g., refresh, RowHammer protection, memory scrubbing) to reliably operate modern DRAM chips. Implementing new maintenance operations often necessitates modifications in the DRAM interface, memory controller, and potentially other system components. Such modifications are only possible with a new DRAM standard, which takes a long time to develop, likely leading to slow progress in the adoption of new architectural techniques in DRAM chips. We propose a new low-cost DRAM architecture, Self-Managing DRAM (SMD), that enables autonomous in-DRAM maintenance operations by transferring the responsibility for controlling maintenance operations from the memory controller to the SMD chip. To enable autonomous maintenance operations, we make a single modification to the DRAM interface, such that an SMD chip rejects memory controller accesses to DRAM regions under maintenance, while allowing memory accesses to others. Thus, SMD enables 1) implementing new in-DRAM maintenance mechanisms (or modifying existing ones) with no further changes in the DRAM interface or other system components, and 2) overlapping the latency of a maintenance operation in one DRAM region with the latency of accessing data in another. We evaluate SMD and show that it 1) can be implemented without adding new pins to the DDRx interface with low latency and area overhead, 2) achieves 4.1% average speedup across 20 four-core memory-intensive workloads over a DDR4-based system/DRAM co-design technique that intelligently parallelizes maintenance operations with memory accesses, and 3) guarantees forward progress for rejected memory accesses. We believe and hope SMD can enable innovations in DRAM architecture to rapidly come to fruition. We open source all SMD source code and data at https://github.com/CMU-SAFARI/SelfManagingDRAM.

cs.AR↗

arXiv2025

MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem

Raw signal genome analysis (RSGA) has emerged as a promising approach to enable real-time genome analysis by directly analyzing raw electrical signals. However, rapid advancements in sequencing technologies make it increasingly difficult for software-based RSGA to match the throughput of raw signal generation. This paper demonstrates that while hardware acceleration techniques can significantly accelerate RSGA, the high volume of genomic data shifts the performance and energy bottleneck from computation to I/O data movement. As sequencing throughput increases, I/O overhead becomes the main contributor to both runtime and energy consumption. Therefore, there is a need to design a high-performance, energy-efficient system for RSGA that can both alleviate the data movement bottleneck and provide large acceleration capabilities. We propose MARS, a storage-centric system that leverages the heterogeneous resources within modern storage systems (e.g., storage-internal DRAM, storage controller, flash chips) alongside their large storage capacity to tackle both data movement and computational overheads of RSGA in an area-efficient and low-cost manner. MARS accelerates RSGA through a novel hardware/software co-design approach. First, MARS modifies the RSGA pipeline via two filtering mechanisms and a quantization scheme, reducing hardware demands and optimizing for in-storage execution. Second, MARS accelerates the RSGA steps directly within the storage by leveraging both Processing-Near-Memory and Processing-Using-Memory paradigms. Third, MARS orchestrates the execution of all steps to fully exploit in-storage parallelism and minimize data movement. Our evaluation shows that MARS outperforms basecalling-based software and hardware-accelerated state-of-the-art read mapping pipelines by 93x and 40x, on average across different datasets, while reducing their energy consumption by 427x and 72x.

cs.AR↗