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Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals directly if a reference genome is unknown due to a lack of accurate mechanisms to handle increased noise in pairwise raw signal comparison. Our goal is to enable the direct analysis of raw signals without a reference genome. To this end, we propose Rawsamble, the first mechanism that can 1) identify regions of similarity between all raw signal pairs, known as all-vs-all overlapping, using a hash-based search mechanism and 2) use these to construct genomes from scratch, called de novo assembly. Our extensive evaluations across multiple genomes of varying sizes show that Rawsamble provides a significant speedup (on average by 16.36x and up to 41.59x) and reduces peak memory usage (on average by 11.73x and up to by 41.99x) compared to a conventional genome assembly pipeline using the state-of-the-art tools for basecalling (Dorado's fastest mode) and overlapping (minimap2) on a CPU. We find that 36.57% of overlapping pairs generated by Rawsamble are identical to those generated by minimap2. Using the overlaps from Rawsamble, we construct the first de novo assemblies directly from raw signals without basecalling. We show that we can construct contiguous assembly segments (unitigs) up to 2.7 million bases in length (half the genome length of E. coli). We identify previously unexplored directions that can be enabled by finding overlaps and constructing de novo assemblies. Rawsamble is available at https://github.com/CMU-SAFARI/RawHash. We also provide the scripts to fully reproduce our results on our GitHub page.

Early detection of autism, a neurodevelopmental disorder marked by social communication challenges, is crucial for timely intervention. Recent advancements have utilized naturalistic home videos captured via the mobile application GuessWhat. Through interactive games played between children and their guardians, GuessWhat has amassed over 3,000 structured videos from 382 children, both diagnosed with and without Autism Spectrum Disorder (ASD). This collection provides a robust dataset for training computer vision models to detect ASD-related phenotypic markers, including variations in emotional expression, eye contact, and head movements. We have developed a protocol to curate high-quality videos from this dataset, forming a comprehensive training set. Utilizing this set, we trained individual LSTM-based models using eye gaze, head positions, and facial landmarks as input features, achieving test AUCs of 86%, 67%, and 78%, respectively. To boost diagnostic accuracy, we applied late fusion techniques to create ensemble models, improving the overall AUC to 90%. This approach also yielded more equitable results across different genders and age groups. Our methodology offers a significant step forward in the early detection of ASD by potentially reducing the reliance on subjective assessments and making early identification more accessibly and equitable.

Knowledge graphs (KGs) have achieved significant attention in recent years, particularly in the area of the Semantic Web as well as gaining popularity in other application domains such as data mining and search engines. Simultaneously, there has been enormous progress in the development of different types of heterogeneous hardware, impacting the way KGs are processed. The aim of this paper is to provide a systematic literature review of knowledge graph hardware acceleration. For this, we present a classification of the primary areas in knowledge graph technology that harnesses different hardware units for accelerating certain knowledge graph functionalities. We then extensively describe respective works, focusing on how KG related schemes harness modern hardware accelerators. Based on our review, we identify various research gaps and future exploratory directions that are anticipated to be of significant value both for academics and industry practitioners.

The roadmap is organized into several thematic sections, outlining current computing challenges, discussing the neuromorphic computing approach, analyzing mature and currently utilized technologies, providing an overview of emerging technologies, addressing material challenges, exploring novel computing concepts, and finally examining the maturity level of emerging technologies while determining the next essential steps for their advancement., Comment: 90 pages, 22 figures, roadmap, neuromorphic

Metagenomics has led to significant advances in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative abundances. These tasks require searching large metagenomic databases. Metagenomic analysis suffers from significant data movement overhead due to moving large amounts of low-reuse data from the storage system. In-storage processing can be a fundamental solution for reducing this overhead. However, designing an in-storage processing system for metagenomics is challenging because existing approaches to metagenomic analysis cannot be directly implemented in storage effectively due to the hardware limitations of modern SSDs. We propose MegIS, the first in-storage processing system designed to significantly reduce the data movement overhead of the end-to-end metagenomic analysis pipeline. MegIS is enabled by our lightweight design that effectively leverages and orchestrates processing inside and outside the storage system. We address in-storage processing challenges for metagenomics via specialized and efficient 1) task partitioning, 2) data/computation flow coordination, 3) storage technology-aware algorithmic optimizations, 4) data mapping, and 5) lightweight in-storage accelerators. MegIS's design is flexible, capable of supporting different types of metagenomic input datasets, and can be integrated into various metagenomic analysis pipelines. Our evaluation shows that MegIS outperforms the state-of-the-art performance- and accuracy-optimized software metagenomic tools by 2.7$\times$-37.2$\times$ and 6.9$\times$-100.2$\times$, respectively, while matching the accuracy of the accuracy-optimized tool. MegIS achieves 1.5$\times$-5.1$\times$ speedup compared to the state-of-the-art metagenomic hardware-accelerated (using processing-in-memory) tool, while achieving significantly higher accuracy., Comment: To appear in ISCA 2024. arXiv admin note: substantial text overlap with arXiv:2311.12527

We 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), described in JEDEC DDR5 specification's April 2024 update. Unlike prior state-of-the-art that advises the memory controller to periodically issue refresh management (RFM) commands, which provides the DRAM chip with time to perform refreshes, PRAC introduces a new back-off signal. PRAC's back-off signal propagates from the DRAM chip to the memory controller and forces the memory controller to 1) stop serving requests and 2) issue RFM commands. As a result, RFM commands are issued when needed as opposed to periodically, reducing RFM's overheads. We analyze PRAC in four steps. First, we define an adversarial access pattern that represents the worst-case for PRAC's security. Second, we investigate PRAC's configurations and security implications. Our analyses show that PRAC can be configured for secure operation as long as no bitflip occurs before accessing a memory location 10 times. Third, we evaluate the performance impact of PRAC and compare it against prior works using Ramulator 2.0. Our analysis shows that while PRAC incurs less than 13% performance overhead for today's DRAM chips, its performance overheads can reach up to 94% for future DRAM chips that are more vulnerable to read disturbance bitflips. Fourth, we define an availability adversarial access pattern that exacerbates PRAC's performance overhead to perform a memory performance attack, demonstrating that such an adversarial pattern can hog up to 94% of DRAM throughput and degrade system throughput by up to 95%. We discuss PRAC's implications on future systems and foreshadow future research directions. To aid future research, we open-source our implementations and scripts at https://github.com/CMU-SAFARI/ramulator2., Comment: To appear in DRAMSec 2024

Load instructions often limit instruction-level parallelism (ILP) in modern processors due to data and resource dependences they cause. Prior techniques like Load Value Prediction (LVP) and Memory Renaming (MRN) mitigate load data dependence by predicting the data value of a load instruction. However, they fail to mitigate load resource dependence as the predicted load instruction gets executed nonetheless. Our goal in this work is to improve ILP by mitigating both load data dependence and resource dependence. To this end, we propose a purely-microarchitectural technique called Constable, that safely eliminates the execution of load instructions. Constable dynamically identifies load instructions that have repeatedly fetched the same data from the same load address. We call such loads likely-stable. For every likely-stable load, Constable (1) tracks modifications to its source architectural registers and memory location via lightweight hardware structures, and (2) eliminates the execution of subsequent instances of the load instruction until there is a write to its source register or a store or snoop request to its load address. Our extensive evaluation using a wide variety of 90 workloads shows that Constable improves performance by 5.1% while reducing the core dynamic power consumption by 3.4% on average over a strong baseline system that implements MRN and other dynamic instruction optimizations (e.g., move and zero elimination, constant and branch folding). In presence of 2-way simultaneous multithreading (SMT), Constable's performance improvement increases to 8.8% over the baseline system. When combined with a state-of-the-art load value predictor (EVES), Constable provides an additional 3.7% and 7.8% average performance benefit over the load value predictor alone, in the baseline system without and with 2-way SMT, respectively., Comment: To appear in the proceedings of 51st International Symposium on Computer Architecture (ISCA)

Memory isolation is a critical property for system reliability, security, and safety. We demonstrate RowPress, a DRAM read disturbance phenomenon different from the well-known RowHammer. RowPress induces bitflips by keeping a DRAM row open for a long period of time instead of repeatedly opening and closing the row. We experimentally characterize RowPress bitflips, showing their widespread existence in commodity off-the-shelf DDR4 DRAM chips. We demonstrate RowPress bitflips in a real system that already has RowHammer protection, and propose effective mitigation techniques that protect DRAM against both RowHammer and RowPress., Comment: To Appear in IEEE MICRO Top Picks Special Issue (July-August 2024). arXiv admin note: substantial text overlap with arXiv:2306.17061

DRAM read disturbance can break memory isolation, a fundamental property to ensure system robustness (i.e., reliability, security, safety). RowHammer and RowPress are two different DRAM read disturbance phenomena. RowHammer induces bitflips in physically adjacent victim DRAM rows by repeatedly opening and closing an aggressor DRAM row, while RowPress induces bitflips by keeping an aggressor DRAM row open for a long period of time. In this study, we characterize a DRAM access pattern that combines RowHammer and RowPress in 84 real DDR4 DRAM chips from all three major DRAM manufacturers. Our key results show that 1) this combined RowHammer and RowPress pattern takes significantly smaller amount of time (up to 46.1% faster) to induce the first bitflip compared to the state-of-the-art RowPress pattern, and 2) at the minimum aggressor row activation count to induce at least one bitflip, the bits that flip are different across RowHammer, RowPress, and the combined patterns. Based on our results, we provide a key hypothesis that the read disturbance effect caused by RowPress from one of the two aggressor rows in a double-sided pattern is much more significant than the other., Comment: To appear at DSN Disrupt 2024 (June 2024)

We experimentally analyze the computational capability of commercial off-the-shelf (COTS) DRAM chips and the robustness of these capabilities under various timing delays between DRAM commands, data patterns, temperature, and voltage levels. We extensively characterize 120 COTS DDR4 chips from two major manufacturers. We highlight four key results of our study. First, COTS DRAM chips are capable of 1) simultaneously activating up to 32 rows (i.e., simultaneous many-row activation), 2) executing a majority of X (MAJX) operation where X>3 (i.e., MAJ5, MAJ7, and MAJ9 operations), and 3) copying a DRAM row (concurrently) to up to 31 other DRAM rows, which we call Multi-RowCopy. Second, storing multiple copies of MAJX's input operands on all simultaneously activated rows drastically increases the success rate (i.e., the percentage of DRAM cells that correctly perform the computation) of the MAJX operation. For example, MAJ3 with 32-row activation (i.e., replicating each MAJ3's input operands 10 times) has a 30.81% higher average success rate than MAJ3 with 4-row activation (i.e., no replication). Third, data pattern affects the success rate of MAJX and Multi-RowCopy operations by 11.52% and 0.07% on average. Fourth, simultaneous many-row activation, MAJX, and Multi-RowCopy operations are highly resilient to temperature and voltage changes, with small success rate variations of at most 2.13% among all tested operations. We believe these empirical results demonstrate the promising potential of using DRAM as a computation substrate. To aid future research and development, we open-source our infrastructure at https://github.com/CMU-SAFARI/SiMRA-DRAM., Comment: To appear in DSN 2024

Reinforcement Learning (RL) trains agents to learn optimal behavior by maximizing reward signals from experience datasets. However, RL training often faces memory limitations, leading to execution latencies and prolonged training times. To overcome this, SwiftRL explores Processing-In-Memory (PIM) architectures to accelerate RL workloads. We achieve near-linear performance scaling by implementing RL algorithms like Tabular Q-learning and SARSA on UPMEM PIM systems and optimizing for hardware. Our experiments on OpenAI GYM environments using UPMEM hardware demonstrate superior performance compared to CPU and GPU implementations.

RowHammer is a major read disturbance mechanism in DRAM where repeatedly accessing (hammering) a row of DRAM cells (DRAM row) induces bitflips in other physically nearby DRAM rows. RowHammer solutions perform preventive actions (e.g., refresh neighbor rows of the hammered row) that mitigate such bitflips to preserve memory isolation, a fundamental building block of security and privacy in modern computing systems. However, preventive actions induce non-negligible memory request latency and system performance overheads as they interfere with memory requests. As shrinking technology node size over DRAM chip generations exacerbates RowHammer, the overheads of RowHammer solutions become prohibitively expensive. As a result, a malicious program can effectively hog the memory system and deny service to benign applications by causing many RowHammer-preventive actions. In this work, we tackle the performance overheads of RowHammer solutions by tracking and throttling the generators of memory accesses that trigger RowHammer solutions. To this end, we propose BreakHammer. BreakHammer 1) observes the time-consuming RowHammer-preventive actions of existing RowHammer mitigation mechanisms, 2) identifies hardware threads that trigger many of these actions, and 3) reduces the memory bandwidth usage of each identified thread. As such, BreakHammer significantly reduces the number of RowHammer-preventive actions performed, thereby improving 1) system performance and DRAM energy, and 2) reducing the maximum slowdown induced on a benign application, with near-zero area overhead. Our extensive evaluations demonstrate that BreakHammer effectively reduces the negative performance, energy, and fairness effects of eight RowHammer mitigation mechanisms. To foster further research we open-source our BreakHammer implementation and scripts at https://github.com/CMU-SAFARI/BreakHammer., Comment: To appear in MICRO'24

The adoption of processing-in-memory (PiM) architectures has been gaining momentum because they provide high performance and low energy consumption by alleviating the data movement bottleneck. Yet, the security of such architectures has not been thoroughly explored. The adoption of PiM solutions provides a new way to directly access main memory, which malicious user applications can exploit. We show that this new way to access main memory opens opportunities for high-throughput timing attacks that are hard-to-mitigate without significant performance overhead. We introduce IMPACT, a set of high-throughput main memory-based timing attacks that leverage characteristics of PiM architectures to establish covert and side channels. IMPACT enables high-throughput communication and private information leakage by exploiting the shared DRAM row buffer. To achieve high throughput, IMPACT (i) eliminates cache bypassing steps required by processor-centric main memory and cache-based timing attacks and (ii) leverages the intrinsic parallelism of PiM operations. We showcase two applications of IMPACT. First, we build two covert-channel attacks that run on the host CPU and leverage different PiM approaches to gain direct and fast access to main memory and establish high-throughput communication covert channels. Second, we showcase a side-channel attack that leaks private information of concurrently running victim applications that are accelerated with PiM. Our results demonstrate that (i) our covert channels achieve 12.87 Mb/s and 14.16 Mb/s communication throughput, respectively, which is up to 4.91x and 5.41x faster than the state-of-the-art main memory-based covert channels, and (ii) our side-channel attack allows the attacker to leak secrets with a low error rate. To avoid such covert and side channels in emerging PiM systems, we propose and evaluate three defenses.

This work investigates a new erase scheme in NAND flash memory to improve the lifetime and performance of modern solid-state drives (SSDs). In NAND flash memory, an erase operation applies a high voltage (e.g., > 20 V) to flash cells for a long time (e.g., > 3.5 ms), which degrades cell endurance and potentially delays user I/O requests. While a large body of prior work has proposed various techniques to mitigate the negative impact of erase operations, no work has yet investigated how erase latency should be set to fully exploit the potential of NAND flash memory; most existing techniques use a fixed latency for every erase operation which is set to cover the worst-case operating conditions. To address this, we propose AERO (Adaptive ERase Operation), a new erase scheme that dynamically adjusts erase latency to be just long enough for reliably erasing target cells, depending on the cells' current erase characteristics. AERO accurately predicts such near-optimal erase latency based on the number of fail bits during an erase operation. To maximize its benefits, we further optimize AERO in two aspects. First, at the beginning of an erase operation, AERO attempts to erase the cells for a short time (e.g., 1 ms), which enables AERO to always obtain the number of fail bits necessary to accurately predict the near-optimal erase latency. Second, AERO aggressively yet safely reduces erase latency by leveraging a large reliability margin present in modern SSDs. We demonstrate the feasibility and reliability of AERO using 160 real 3D NAND flash chips, showing that it enhances SSD lifetime over the conventional erase scheme by 43% without change to existing NAND flash chips. Our system-level evaluation using eleven real-world workloads shows that an AERO-enabled SSD reduces read tail latency by 34% on average over a state-of-the-art technique., Comment: Accepted for publication at Proceedings of the 29th International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), 2024

Modern Machine Learning (ML) training on large-scale datasets is a very time-consuming workload. It relies on the optimization algorithm Stochastic Gradient Descent (SGD) due to its effectiveness, simplicity, and generalization performance. Processor-centric architectures (e.g., CPUs, GPUs) commonly used for modern ML training workloads based on SGD are bottlenecked by data movement between the processor and memory units due to the poor data locality in accessing large datasets. As a result, processor-centric architectures suffer from low performance and high energy consumption while executing ML training workloads. Processing-In-Memory (PIM) is a promising solution to alleviate the data movement bottleneck by placing the computation mechanisms inside or near memory. Our goal is to understand the capabilities of popular distributed SGD algorithms on real-world PIM systems to accelerate data-intensive ML training workloads. To this end, we 1) implement several representative centralized parallel SGD algorithms on the real-world UPMEM PIM system, 2) rigorously evaluate these algorithms for ML training on large-scale datasets in terms of performance, accuracy, and scalability, 3) compare to conventional CPU and GPU baselines, and 4) discuss implications for future PIM hardware and highlight the need for a shift to an algorithm-hardware codesign. Our results demonstrate three major findings: 1) The UPMEM PIM system can be a viable alternative to state-of-the-art CPUs and GPUs for many memory-bound ML training workloads, especially when operations and datatypes are natively supported by PIM hardware, 2) it is important to carefully choose the optimization algorithms that best fit PIM, and 3) the UPMEM PIM system does not scale approximately linearly with the number of nodes for many data-intensive ML training workloads. We open source all our code to facilitate future research., Comment: "PIM-Opt: Demystifying Distributed Optimization Algorithms on a Real-World Processing-In-Memory System" in Proceedings of the 33rd International Conference on Parallel Architectures and Compilation Techniques (PACT), Long Beach, CA, USA, October 2024

Virtual memory is a cornerstone of modern computing systems.Introduced as one of the earliest instances of hardware-software co-design, VM facilitates programmer-transparent memory man agement, data sharing, process isolation and memory protection. Evaluating the efficiency of various virtual memory (VM) designs is crucial (i) given their significant impact on the system, including the CPU caches, the main memory, and the storage device and (ii) given that different system architectures might benefit from various VM techniques. Such an evaluation is not straightforward, as it heavily hinges on modeling the interplay between different VM techniques and the interactions of VM with the system architecture. Modern simulators, however, struggle to keep up with the rapid VM research developments, lacking the capability to model a wide range of contemporary VM techniques and their interactions. To this end, we present Virtuoso, an open-source, comprehensive and modular simulation framework that models various VM designs to establish a common ground for virtual memory research. We demonstrate the versatility and the potential of Virtuoso with four new case studies. Virtuoso is freely open-source and can be found at https://github.com/CMU-SAFARI/Virtuoso.

Processing-using-DRAM (PUD) architectures impose a restrictive data layout and alignment for their operands, where source and destination operands (i) must reside in the same DRAM subarray (i.e., a group of DRAM rows sharing the same row buffer and row decoder) and (ii) are aligned to the boundaries of a DRAM row. However, standard memory allocation routines (i.e., malloc, posix_memalign, and huge pages-based memory allocation) fail to meet the data layout and alignment requirements for PUD architectures to operate successfully. To allow the memory allocation API to influence the OS memory allocator and ensure that memory objects are placed within specific DRAM subarrays, we propose a new lazy data allocation routine (in the kernel) for PUD memory objects called PUMA. The key idea of PUMA is to use the internal DRAM mapping information together with huge pages and then split huge pages into finer-grained allocation units that are (i) aligned to the page address and size and (ii) virtually contiguous. We implement PUMA as a kernel module using QEMU and emulate a RISC-V machine running Fedora 33 with v5.9.0 Linux Kernel. We emulate the implementation of a PUD system capable of executing row copy operations (as in RowClone) and Boolean AND/OR/NOT operations (as in Ambit). In our experiments, such an operation is performed in the host CPU if a given operation cannot be executed in our PUD substrate (due to data misalignment). PUMA significantly outperforms the baseline memory allocators for all evaluated microbenchmarks and allocation sizes.

Processing-using-DRAM (PUD) is a processing-in-memory (PIM) approach that uses a DRAM array's massive internal parallelism to execute very-wide data-parallel operations, in a single-instruction multiple-data (SIMD) fashion. However, DRAM rows' large and rigid granularity limit the effectiveness and applicability of PUD in three ways. First, since applications have varying degrees of SIMD parallelism, PUD execution often leads to underutilization, throughput loss, and energy waste. Second, most PUD architectures are limited to the execution of parallel map operations. Third, the need to feed the wide DRAM row with tens of thousands of data elements combined with the lack of adequate compiler support for PUD systems create a programmability barrier. Our goal is to design a flexible PUD system that overcomes the limitations caused by the large and rigid granularity of PUD. To this end, we propose MIMDRAM, a hardware/software co-designed PUD system that introduces new mechanisms to allocate and control only the necessary resources for a given PUD operation. The key idea of MIMDRAM is to leverage fine-grained DRAM (i.e., the ability to independently access smaller segments of a large DRAM row) for PUD computation. MIMDRAM exploits this key idea to enable a multiple-instruction multiple-data (MIMD) execution model in each DRAM subarray. We evaluate MIMDRAM using twelve real-world applications and 495 multi-programmed application mixes. Our evaluation shows that MIMDRAM provides 34x the performance, 14.3x the energy efficiency, 1.7x the throughput, and 1.3x the fairness of a state-of-the-art PUD framework, along with 30.6x and 6.8x the energy efficiency of a high-end CPU and GPU, respectively. MIMDRAM adds small area cost to a DRAM chip (1.11%) and CPU die (0.6%)., Comment: Extended version of HPCA 2024 paper. arXiv admin note: text overlap with arXiv:2109.05881 by other authors

Read disturbance in modern DRAM chips is a widespread phenomenon and is reliably used for breaking memory isolation, a fundamental building block for building robust systems. RowHammer and RowPress are two examples of read disturbance in DRAM where repeatedly accessing (hammering) or keeping active (pressing) a memory location induces bitflips in other memory locations. Unfortunately, shrinking technology node size exacerbates read disturbance in DRAM chips over generations. As a result, existing defense mechanisms suffer from significant performance and energy overheads, limited effectiveness, or prohibitively high hardware complexity. In this paper, we tackle these shortcomings by leveraging the spatial variation in read disturbance across different memory locations in real DRAM chips. To do so, we 1) present the first rigorous real DRAM chip characterization study of spatial variation of read disturbance and 2) propose Sv\"ard, a new mechanism that dynamically adapts the aggressiveness of existing solutions based on the row-level read disturbance profile. Our experimental characterization on 144 real DDR4 DRAM chips representing 10 chip designs demonstrates a large variation in read disturbance vulnerability across different memory locations: in the part of memory with the worst read disturbance vulnerability, 1) up to 2x the number of bitflips can occur and 2) bitflips can occur at an order of magnitude fewer accesses, compared to the memory locations with the least vulnerability to read disturbance. Sv\"ard leverages this variation to reduce the overheads of five state-of-the-art read disturbance solutions, and thus significantly increases system performance., Comment: A shorter version of this work is to appear at the 30th IEEE International Symposium on High-Performance Computer Architecture (HPCA-30), 2024

We propose a new RowHammer mitigation mechanism, CoMeT, that prevents RowHammer bitflips with low area, performance, and energy costs in DRAM-based systems at very low RowHammer thresholds. The key idea of CoMeT is to use low-cost and scalable hash-based counters to track DRAM row activations. CoMeT uses the Count-Min Sketch technique that maps each DRAM row to a group of counters, as uniquely as possible, using multiple hash functions. When a DRAM row is activated, CoMeT increments the counters mapped to that DRAM row. Because the mapping from DRAM rows to counters is not completely unique, activating one row can increment one or more counters mapped to another row. Thus, CoMeT may overestimate, but never underestimates, a DRAM row's activation count. This property of CoMeT allows it to securely prevent RowHammer bitflips while properly configuring its hash functions reduces overestimations. As a result, CoMeT 1) implements substantially fewer counters than the number of DRAM rows in a DRAM bank and 2) does not significantly overestimate a DRAM row's activation count. Our comprehensive evaluations show that CoMeT prevents RowHammer bitflips with an average performance overhead of only 4.01% across 61 benign single-core workloads for a very low RowHammer threshold of 125, normalized to a system with no RowHammer mitigation. CoMeT achieves a good trade-off between performance, energy, and area overheads. Compared to the best-performing state-of-the-art mitigation, CoMeT requires 74.2x less area overhead at the RowHammer threshold 125 and incurs a small performance overhead on average for all RowHammer thresholds. Compared to the best-performing low-area-cost mechanism, at a very low RowHammer threshold of 125, CoMeT improves performance by up to 39.1% while incurring a similar area overhead. CoMeT is openly and freely available at https://github.com/CMU-SAFARI/CoMeT., Comment: To appear at HPCA 2024

Processing-using-DRAM (PuD) is an emerging paradigm that leverages the analog operational properties of DRAM circuitry to enable massively parallel in-DRAM computation. PuD has the potential to reduce or eliminate costly data movement between processing elements and main memory. Prior works experimentally demonstrate three-input MAJ (MAJ3) and two-input AND and OR operations in commercial off-the-shelf (COTS) DRAM chips. Yet, demonstrations on COTS DRAM chips do not provide a functionally complete set of operations. We experimentally demonstrate that COTS DRAM chips are capable of performing 1) functionally-complete Boolean operations: NOT, NAND, and NOR and 2) many-input (i.e., more than two-input) AND and OR operations. We present an extensive characterization of new bulk bitwise operations in 256 off-the-shelf modern DDR4 DRAM chips. We evaluate the reliability of these operations using a metric called success rate: the fraction of correctly performed bitwise operations. Among our 19 new observations, we highlight four major results. First, we can perform the NOT operation on COTS DRAM chips with a 98.37% success rate on average. Second, we can perform up to 16-input NAND, NOR, AND, and OR operations on COTS DRAM chips with high reliability (e.g., 16-input NAND, NOR, AND, and OR with an average success rate of 94.94%, 95.87%, 94.94%, and 95.85%, respectively). Third, data pattern only slightly affects bitwise operations. Our results show that executing NAND, NOR, AND, and OR operations with random data patterns decreases the success rate compared to all logic-1/logic-0 patterns by 1.39%, 1.97%, 1.43%, and 1.98%, respectively. Fourth, bitwise operations are highly resilient to temperature changes, with small success rate fluctuations of at most 1.66% when the temperature is increased from 50C to 95C. We open-source our infrastructure at https://github.com/CMU-SAFARI/FCDRAM, Comment: A shorter version of this work is to appear at the 30th IEEE International Symposium on High-Performance Computer Architecture (HPCA-30), 2024

Graph Neural Networks (GNNs) are emerging ML models to analyze graph-structure data. Graph Neural Network (GNN) execution involves both compute-intensive and memory-intensive kernels, the latter dominates the total time, being significantly bottlenecked by data movement between memory and processors. Processing-In-Memory (PIM) systems can alleviate this data movement bottleneck by placing simple processors near or inside to memory arrays. In this work, we introduce PyGim, an efficient ML library that accelerates GNNs on real PIM systems. We propose intelligent parallelization techniques for memory-intensive kernels of GNNs tailored for real PIM systems, and develop handy Python API for them. We provide hybrid GNN execution, in which the compute-intensive and memory-intensive kernels are executed in processor-centric and memory-centric computing systems, respectively. We extensively evaluate PyGim on a real-world PIM system with 1992 PIM cores using emerging GNN models, and demonstrate that it outperforms its state-of-the-art CPU counterpart on Intel Xeon by on average 3.04x, and achieves higher resource utilization than CPU and GPU systems. Our work provides useful recommendations for software, system and hardware designers. PyGim is publicly available at https://github.com/CMU-SAFARI/PyGim.

The increasing variety and quantity of tagged multimedia content on a variety of online platforms offer a unique opportunity to advance the field of human action recognition. In this study, we utilize 283,582 unique, unlabeled TikTok video clips, categorized into 386 hashtags, to train a domain-specific foundation model for action recognition. We employ VideoMAE V2, an advanced model integrating Masked Autoencoders (MAE) with Vision Transformers (ViT), pre-trained on this diverse collection of unstructured videos. Our model, fine-tuned on established action recognition benchmarks such as UCF101 and HMDB51, achieves state-of-the-art results: 99.05% on UCF101, 86.08% on HMDB51, 85.51% on Kinetics-400, and 74.27% on Something-Something V2 using the ViT-giant backbone. These results highlight the potential of using unstructured and unlabeled videos as a valuable source of diverse and dynamic content for training foundation models. Our investigation confirms that while initial increases in pre-training data volume significantly enhance model performance, the gains diminish as the dataset size continues to expand. Our findings emphasize two critical axioms in self-supervised learning for computer vision: (1) additional pre-training data can yield diminishing benefits for some datasets and (2) quality is more important than quantity in self-supervised learning, especially when building foundation models., Comment: 10 pages

Generational improvements to commodity DRAM throughout half a century have long solidified its prevalence as main memory across the computing industry. However, overcoming today's DRAM technology scaling challenges requires new solutions driven by both DRAM producers and consumers. In this paper, we observe that the separation of concerns between producers and consumers specified by industry-wide DRAM standards is becoming a liability to progress in addressing scaling-related concerns. To understand the problem, we study four key directions for overcoming DRAM scaling challenges using system-memory cooperation: (i) improving memory access latencies; (ii) reducing DRAM refresh overheads; (iii) securely defending against the RowHammer vulnerability; and (iv) addressing worsening memory errors. We find that the single most important barrier to advancement in all four cases is the consumer's lack of insight into DRAM reliability. Based on an analysis of DRAM reliability testing, we recommend revising the separation of concerns to incorporate limited information transparency between producers and consumers. Finally, we propose adopting this revision in a two-step plan, starting with immediate information release through crowdsourcing and publication and culminating in widespread modifications to DRAM standards., Comment: arXiv admin note: substantial text overlap with arXiv:2204.10378

The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models' (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM's capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and other parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.

Data movement between the processor and the main memory is a first-order obstacle against improving performance and energy efficiency in modern systems. To address this obstacle, Processing-using-Memory (PuM) is a promising approach where bulk-bitwise operations are performed leveraging intrinsic analog properties within the DRAM array and massive parallelism across DRAM columns. Unfortunately, 1) modern off-the-shelf DRAM chips do not officially support PuM operations, and 2) existing techniques of performing PuM operations on off-the-shelf DRAM chips suffer from two key limitations. First, these techniques have low success rates, i.e., only a small fraction of DRAM columns can correctly execute PuM operations because they operate beyond manufacturer-recommended timing constraints, causing these operations to be highly susceptible to noise and process variation. Second, these techniques have limited compute primitives, preventing them from fully leveraging parallelism across DRAM columns and thus hindering their performance benefits. We propose PULSAR, a new technique to enable high-success-rate and high-performance PuM operations in off-the-shelf DRAM chips. PULSAR leverages our new observation that a carefully crafted sequence of DRAM commands simultaneously activates up to 32 DRAM rows. PULSAR overcomes the limitations of existing techniques by 1) replicating the input data to improve the success rate and 2) enabling new bulk bitwise operations (e.g., many-input majority, Multi-RowInit, and Bulk-Write) to improve the performance. Our analysis on 120 off-the-shelf DDR4 chips from two major manufacturers shows that PULSAR achieves a 24.18% higher success rate and 121% higher performance over seven arithmetic-logic operations compared to FracDRAM, a state-of-the-art off-the-shelf DRAM-based PuM technique.

Metagenomics has led to significant advancements in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative abundances. These tasks require searching large metagenomic databases containing information on different species' genomes. Metagenomic analysis suffers from significant data movement overhead due to moving large amounts of low-reuse data from the storage system to the rest of the system. In-storage processing can be a fundamental solution for reducing data movement overhead. However, designing an in-storage processing system for metagenomics is challenging because none of the existing approaches can be directly implemented in storage effectively due to the hardware limitations of modern SSDs. We propose MetaStore, the first in-storage processing system designed to significantly reduce the data movement overhead of end-to-end metagenomic analysis. MetaStore is enabled by our lightweight and cooperative design that effectively leverages and orchestrates processing inside and outside the storage system. Through our detailed analysis of the end-to-end metagenomic analysis pipeline and careful hardware/software co-design, we address in-storage processing challenges for metagenomics via specialized and efficient 1) task partitioning, 2) data/computation flow coordination, 3) storage technology-aware algorithmic optimizations, 4) light-weight in-storage accelerators, and 5) data mapping. Our evaluation shows that MetaStore outperforms the state-of-the-art performance- and accuracy-optimized software metagenomic tools by 2.7-37.2$\times$ and 6.9-100.2$\times$, respectively, while matching the accuracy of the accuracy-optimized tool. MetaStore achieves 1.5-5.1$\times$ speedup compared to the state-of-the-art metagenomic hardware-accelerated tool, while achieving significantly higher accuracy.

Metagenomics, the study of genome sequences of diverse organisms cohabiting in a shared environment, has experienced significant advancements across various medical and biological fields. Metagenomic analysis is crucial, for instance, in clinical applications such as infectious disease screening and the diagnosis and early detection of diseases such as cancer. A key task in metagenomics is to determine the species present in a sample and their relative abundances. Currently, the field is dominated by either alignment-based tools, which offer high accuracy but are computationally expensive, or alignment-free tools, which are fast but lack the needed accuracy for many applications. In response to this dichotomy, we introduce MetaTrinity, a tool based on heuristics, to achieve a fundamental improvement in accuracy-runtime tradeoff over existing methods. We benchmark MetaTrinity against two leading metagenomic classifiers, each representing different ends of the performance-accuracy spectrum. On one end, Kraken2, a tool optimized for performance, shows modest accuracy yet a rapid runtime. The other end of the spectrum is governed by Metalign, a tool optimized for accuracy. Our evaluations show that MetaTrinity achieves an accuracy comparable to Metalign while gaining a 4x speedup without any loss in accuracy. This directly equates to a fourfold improvement in runtime-accuracy tradeoff. Compared to Kraken2, MetaTrinity requires a 5x longer runtime yet delivers a 17x improvement in accuracy. This demonstrates a 3.4x enhancement in the accuracy-runtime tradeoff for MetaTrinity. This dual comparison positions MetaTrinity as a broadly applicable solution for metagenomic classification, combining advantages of both ends of the spectrum: speed and accuracy. MetaTrinity is publicly available at https://github.com/CMU-SAFARI/MetaTrinity.

Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most fundamental computational steps in most genomic analyses. Due to its high computational complexity, optimized exact and heuristic algorithms are still being developed. We find that these methods are highly sensitive to the underlying data, its quality, and various hyperparameters. Despite their wide use, no in-depth analysis has been performed, potentially falsely discarding genetic sequences from further analysis and unnecessarily inflating computational costs. We provide the first analysis and benchmark of this heterogeneity. We deliver an actionable overview of the 11 most widely used state-of-the-art methods for comparing genomic sequences. We also inform readers about their advantages and downsides using thorough experimental evaluation and different real datasets from all major manufacturers (i.e., Illumina, ONT, and PacBio). SequenceLab is publicly available at https://github.com/CMU-SAFARI/SequenceLab.

With the recent move towards sequencing of accurate long reads, finding solutions that support efficient analysis of these reads becomes more necessary. The long execution time required for sequence alignment of long reads negatively affects genomic studies relying on sequence alignment. Although pre-alignment filtering as an extra step before alignment was recently introduced to mitigate sequence alignment for short reads, these filters do not work as efficiently for long reads. Moreover, even with efficient pre-alignment filters, the overall end-to-end (i.e., filtering + original alignment) execution time of alignment for long reads remains high, while the filtering step is now a major portion of the end-to-end execution time. Our paper makes three contributions. First, it identifies data movement of sequences between memory units and computing units as the main source of inefficiency for pre-alignment filters of long reads. This is because although filters reject many of these long sequencing pairs before they get to the alignment stage, they still require a huge cost regarding time and energy consumption for the large data transferred between memory and processor. Second, this paper introduces an adaptation of a short-read pre-alignment filtering algorithm suitable for long reads. We call this LongGeneGuardian. Finally, it presents Filter-Fuse as an architecture that supports LongGeneGuardian inside the memory. FilterFuse exploits the Computation-In-Memory computing paradigm, eliminating the cost of data movement in LongGeneGuardian. Our evaluations show that FilterFuse improves the execution time of filtering by 120.47x for long reads compared to State-of-the-Art (SoTA) filter, SneakySnake. FilterFuse also improves the end-to-end execution time of sequence alignment by up to 49.14x and 5207.63x compared to SneakySnake with SoTA aligner and only SoTA aligner, respectively.

We experimentally demonstrate the effects of read disturbance (RowHammer and RowPress) and uncover the inner workings of undocumented read disturbance defense mechanisms in High Bandwidth Memory (HBM). Detailed characterization of six real HBM2 DRAM chips in two different FPGA boards shows that (1) the read disturbance vulnerability significantly varies between different HBM2 chips and between different components (e.g., 3D-stacked channels) inside a chip, (2) DRAM rows at the end and in the middle of a bank are more resilient to read disturbance, (3) fewer additional activations are sufficient to induce more read disturbance bitflips in a DRAM row if the row exhibits the first bitflip at a relatively high activation count, (4) a modern HBM2 chip implements undocumented read disturbance defenses that track potential aggressor rows based on how many times they are activated. We describe how our findings could be leveraged to develop more powerful read disturbance attacks and more efficient defense mechanisms. We open source all our code and data to facilitate future research at https://github.com/CMU-SAFARI/HBM-Read-Disturbance., Comment: To appear in DSN 2024

To ease the programmability of PIM architectures, we propose DaPPA(data-parallel processing-in-memory architecture), a framework that can, for a given application, automatically distribute input and gather output data, handle memory management, and parallelize work across the DPUs. The key idea behind DaPPA is to remove the responsibility of managing hardware resources from the programmer by providing an intuitive data-parallel pattern-based programming interface that abstracts the hardware components of the UPMEM system. Using this key idea, DaPPA transforms a data-parallel pattern-based application code into the appropriate UPMEM-target code, including the required APIs for data management and code partition, which can then be compiled into a UPMEM-based binary transparently from the programmer. While generating UPMEM-target code, DaPPA implements several code optimizations to improve end-to-end performance.

We introduce ABACuS, a new low-cost hardware-counter-based RowHammer mitigation technique that performance-, energy-, and area-efficiently scales with worsening RowHammer vulnerability. We observe that both benign workloads and RowHammer attacks tend to access DRAM rows with the same row address in multiple DRAM banks at around the same time. Based on this observation, ABACuS's key idea is to use a single shared row activation counter to track activations to the rows with the same row address in all DRAM banks. Unlike state-of-the-art RowHammer mitigation mechanisms that implement a separate row activation counter for each DRAM bank, ABACuS implements fewer counters (e.g., only one) to track an equal number of aggressor rows. Our evaluations show that ABACuS securely prevents RowHammer bitflips at low performance/energy overhead and low area cost. We compare ABACuS to four state-of-the-art mitigation mechanisms. At a near-future RowHammer threshold of 1000, ABACuS incurs only 0.58% (0.77%) performance and 1.66% (2.12%) DRAM energy overheads, averaged across 62 single-core (8-core) workloads, requiring only 9.47 KiB of storage per DRAM rank. At the RowHammer threshold of 1000, the best prior low-area-cost mitigation mechanism incurs 1.80% higher average performance overhead than ABACuS, while ABACuS requires 2.50X smaller chip area to implement. At a future RowHammer threshold of 125, ABACuS performs very similarly to (within 0.38% of the performance of) the best prior performance- and energy-efficient RowHammer mitigation mechanism while requiring 22.72X smaller chip area. ABACuS is freely and openly available at https://github.com/CMU-SAFARI/ABACuS., Comment: To appear in USENIX Security '24

Nanopore sequencers generate raw electrical signals representing the contents of a biological sequence molecule passing through the nanopore. These signals can be analyzed directly, avoiding basecalling entirely. We observe that while existing proposals for raw signal analysis typically do well in all metrics for small genomes (e.g., viral genomes), they all perform poorly for large genomes (e.g., the human genome). Our goal is to analyze raw nanopore signals in an accurate, fast, and scalable manner. To this end, we propose RawAlign, the first work to integrate fine-grained signal alignment into the state-of-the-art raw signal mapper. To enable accurate, fast, and scalable mapping with alignment, RawAlign implements three algorithmic improvements and hardware acceleration via a vectorized implementation of fine-grained alignment. Together, these significantly reduce the overhead of typically computationally expensive fine-grained alignment. Our extensive evaluations on different use cases and various datasets show RawAlign provides 1) the most accurate mapping for large genomes and 2) and on-par performance compared to RawHash (between 0.80x-1.08x), while achieving better performance than UNCALLED and Sigmap by on average (geo. mean) 2.83x and 2.06x, respectively. Availability: https://github.com/CMU-SAFARI/RawAlign.

Basecalling, an essential step in many genome analysis studies, relies on large Deep Neural Networks (DNNs) to achieve high accuracy. Unfortunately, these DNNs are computationally slow and inefficient, leading to considerable delays and resource constraints in the sequence analysis process. A Computation-In-Memory (CIM) architecture using memristors can significantly accelerate the performance of DNNs. However, inherent device non-idealities and architectural limitations of such designs can greatly degrade the basecalling accuracy, which is critical for accurate genome analysis. To facilitate the adoption of memristor-based CIM designs for basecalling, it is important to (1) conduct a comprehensive analysis of potential CIM architectures and (2) develop effective strategies for mitigating the possible adverse effects of inherent device non-idealities and architectural limitations. This paper proposes Swordfish, a novel hardware/software co-design framework that can effectively address the two aforementioned issues. Swordfish incorporates seven circuit and device restrictions or non-idealities from characterized real memristor-based chips. Swordfish leverages various hardware/software co-design solutions to mitigate the basecalling accuracy loss due to such non-idealities. To demonstrate the effectiveness of Swordfish, we take Bonito, the state-of-the-art (i.e., accurate and fast), open-source basecaller as a case study. Our experimental results using Sword-fish show that a CIM architecture can realistically accelerate Bonito for a wide range of real datasets by an average of 25.7x, with an accuracy loss of 6.01%., Comment: To appear in 56th IEEE/ACM International Symposium on Microarchitecture (MICRO), 2023

Address translation is a performance bottleneck in data-intensive workloads due to large datasets and irregular access patterns that lead to frequent high-latency page table walks (PTWs). PTWs can be reduced by using (i) large hardware TLBs or (ii) large software-managed TLBs. Unfortunately, both solutions have significant drawbacks: increased access latency, power and area (for hardware TLBs), and costly memory accesses, the need for large contiguous memory blocks, and complex OS modifications (for software-managed TLBs). We present Victima, a new software-transparent mechanism that drastically increases the translation reach of the processor by leveraging the underutilized resources of the cache hierarchy. The key idea of Victima is to repurpose L2 cache blocks to store clusters of TLB entries, thereby providing an additional low-latency and high-capacity component that backs up the last-level TLB and thus reduces PTWs. Victima has two main components. First, a PTW cost predictor (PTW-CP) identifies costly-to-translate addresses based on the frequency and cost of the PTWs they lead to. Second, a TLB-aware cache replacement policy prioritizes keeping TLB entries in the cache hierarchy by considering (i) the translation pressure (e.g., last-level TLB miss rate) and (ii) the reuse characteristics of the TLB entries. Our evaluation results show that in native (virtualized) execution environments Victima improves average end-to-end application performance by 7.4% (28.7%) over the baseline four-level radix-tree-based page table design and by 6.2% (20.1%) over a state-of-the-art software-managed TLB, across 11 diverse data-intensive workloads. Victima (i) is effective in both native and virtualized environments, (ii) is completely transparent to application and system software, and (iii) incurs very small area and power overheads on a modern high-end CPU., Comment: To appear in 56th IEEE/ACM International Symposium on Microarchitecture (MICRO), 2023

Data movement between memory and processors is a major bottleneck in modern computing systems. The processing-in-memory (PIM) paradigm aims to alleviate this bottleneck by performing computation inside memory chips. Real PIM hardware (e.g., the UPMEM system) is now available and has demonstrated potential in many applications. However, programming such real PIM hardware remains a challenge for many programmers. This paper presents a new software framework, SimplePIM, to aid programming real PIM systems. The framework processes arrays of arbitrary elements on a PIM device by calling iterator functions from the host and provides primitives for communication among PIM cores and between PIM and the host system. We implement SimplePIM for the UPMEM PIM system and evaluate it on six major applications. Our results show that SimplePIM enables 66.5% to 83.1% reduction in lines of code in PIM programs. The resulting code leads to higher performance (between 10% and 37% speedup) than hand-optimized code in three applications and provides comparable performance in three others. SimplePIM is fully and freely available at https://github.com/CMU-SAFARI/SimplePIM.

Motivation: Read mapping is a computationally expensive process and a major bottleneck in genomics analyses. The performance of read mapping is mainly limited by the performance of three key computational steps: Index Querying, Seed Chaining, and Sequence Alignment. The first step is dominated by how fast and frequent it accesses the main memory (i.e., memory-bound), while the latter two steps are dominated by how fast the CPU can compute their computationally-costly dynamic programming algorithms (i.e., compute-bound). Accelerating these three steps by exploiting new algorithms and new hardware devices is essential to accelerate most genome analysis pipelines that widely use read mapping. Given the large body of work on accelerating Sequence Alignment, this work focuses on significantly improving the remaining steps. Results: We introduce GateSeeder, the first CPU-FPGA-based near-memory acceleration of both short and long read mapping. GateSeeder exploits near-memory computation capability provided by modern FPGAs that couple a reconfigurable compute fabric with high-bandwidth memory (HBM) to overcome the memory-bound and compute-bound bottlenecks. GateSeeder also introduces a new lightweight algorithm for finding the potential matching segment pairs. Using real ONT, HiFi, and Illumina sequences, we experimentally demonstrate that GateSeeder outperforms Minimap2, without performing sequence alignment, by up to 40.3x, 4.8x, and 2.3x, respectively. When performing read mapping with sequence alignment, GateSeeder outperforms Minimap2 by 1.15-4.33x (using KSW2) and by 1.97-13.63x (using WFA-GPU). Availability: https://github.com/CMU-SAFARI/GateSeeder

Computing on encrypted data is a promising approach to reduce data security and privacy risks, with homomorphic encryption serving as a facilitator in achieving this goal. In this work, we accelerate homomorphic operations using the Processing-in- Memory (PIM) paradigm to mitigate the large memory capacity and frequent data movement requirements. Using a real-world PIM system, we accelerate the Brakerski-Fan-Vercauteren (BFV) scheme for homomorphic addition and multiplication. We evaluate the PIM implementations of these homomorphic operations with statistical workloads (arithmetic mean, variance, linear regression) and compare to CPU and GPU implementations. Our results demonstrate 50-100x speedup with a real PIM system (UPMEM) over the CPU and 2-15x over the GPU in vector addition. For vector multiplication, the real PIM system outperforms the CPU by 40-50x. However, it lags 10-15x behind the GPU due to the lack of native sufficiently wide multiplication support in the evaluated first-generation real PIM system. For mean, variance, and linear regression, the real PIM system performance improvements vary between 30x and 300x over the CPU and between 10x and 30x over the GPU, uncovering real PIM system trade-offs in terms of scalability of homomorphic operations for varying amounts of data. We plan to make our implementation open-source in the future., Comment: This work will be presented at IISWC 2023

Summary: Raw nanopore signals can be analyzed while they are being generated, a process known as real-time analysis. Real-time analysis of raw signals is essential to utilize the unique features that nanopore sequencing provides, enabling the early stopping of the sequencing of a read or the entire sequencing run based on the analysis. The state-of-the-art mechanism, RawHash, offers the first hash-based efficient and accurate similarity identification between raw signals and a reference genome by quickly matching their hash values. In this work, we introduce RawHash2, which provides major improvements over RawHash, including a more sensitive quantization and chaining implementation, weighted mapping decisions, frequency filters to reduce ambiguous seed hits, minimizers for hash-based sketching, and support for the R10.4 flow cell version and various data formats such as POD5 and SLOW5. Compared to RawHash, RawHash2 provides better F1 accuracy (on average by 10.57% and up to 20.25%) and better throughput (on average by 4.0x and up to 9.9x) than RawHash. Availability and Implementation: RawHash2 is available at https://github.com/CMU-SAFARI/RawHash. We also provide the scripts to fully reproduce our results on our GitHub page., Comment: Accepted in Bioinformatics: https://doi.org/10.1093/bioinformatics/btae478

We present Ramulator 2.0, a highly modular and extensible DRAM simulator that enables rapid and agile implementation and evaluation of design changes in the memory controller and DRAM to meet the increasing research effort in improving the performance, security, and reliability of memory systems. Ramulator 2.0 abstracts and models key components in a DRAM-based memory system and their interactions into shared interfaces and independent implementations. Doing so enables easy modification and extension of the modeled functions of the memory controller and DRAM in Ramulator 2.0. The DRAM specification syntax of Ramulator 2.0 is concise and human-readable, facilitating easy modifications and extensions. Ramulator 2.0 implements a library of reusable templated lambda functions to model the functionalities of DRAM commands to simplify the implementation of new DRAM standards, including DDR5, LPDDR5, HBM3, and GDDR6. We showcase Ramulator 2.0's modularity and extensibility by implementing and evaluating a wide variety of RowHammer mitigation techniques that require different memory controller design changes. These techniques are added modularly as separate implementations without changing any code in the baseline memory controller implementation. Ramulator 2.0 is rigorously validated and maintains a fast simulation speed compared to existing cycle-accurate DRAM simulators. Ramulator 2.0 is open-sourced under the permissive MIT license at https://github.com/CMU-SAFARI/ramulator2

Memory isolation is critical for system reliability, security, and safety. Unfortunately, read disturbance can break memory isolation in modern DRAM chips. For example, RowHammer is a well-studied read-disturb phenomenon where repeatedly opening and closing (i.e., hammering) a DRAM row many times causes bitflips in physically nearby rows. This paper experimentally demonstrates and analyzes another widespread read-disturb phenomenon, RowPress, in real DDR4 DRAM chips. RowPress breaks memory isolation by keeping a DRAM row open for a long period of time, which disturbs physically nearby rows enough to cause bitflips. We show that RowPress amplifies DRAM's vulnerability to read-disturb attacks by significantly reducing the number of row activations needed to induce a bitflip by one to two orders of magnitude under realistic conditions. In extreme cases, RowPress induces bitflips in a DRAM row when an adjacent row is activated only once. Our detailed characterization of 164 real DDR4 DRAM chips shows that RowPress 1) affects chips from all three major DRAM manufacturers, 2) gets worse as DRAM technology scales down to smaller node sizes, and 3) affects a different set of DRAM cells from RowHammer and behaves differently from RowHammer as temperature and access pattern changes. We demonstrate in a real DDR4-based system with RowHammer protection that 1) a user-level program induces bitflips by leveraging RowPress while conventional RowHammer cannot do so, and 2) a memory controller that adaptively keeps the DRAM row open for a longer period of time based on access pattern can facilitate RowPress-based attacks. To prevent bitflips due to RowPress, we describe and evaluate a new methodology that adapts existing RowHammer mitigation techniques to also mitigate RowPress with low additional performance overhead. We open source all our code and data to facilitate future research on RowPress., Comment: Extended version of the paper "RowPress: Amplifying Read Disturbance in Modern DRAM Chips" at the 50th Annual International Symposium on Computer Architecture (ISCA), 2023

Our ISCA 2014 paper provided the first scientific and detailed characterization, analysis, and real-system demonstration of what is now popularly known as the RowHammer phenomenon (or vulnerability) in modern commodity DRAM chips, which are used as main memory in almost all modern computing systems. It experimentally demonstrated that more than 80% of all DRAM modules we tested from the three major DRAM vendors were vulnerable to the RowHammer read disturbance phenomenon: one can predictably induce bitflips (i.e., data corruption) in real DRAM modules by repeatedly accessing a DRAM row and thus causing electrical disturbance to physically nearby rows. We showed that a simple unprivileged user-level program induced RowHammer bitflips in multiple real systems and suggested that a security attack can be built using this proof-of-concept to hijack control of the system or cause other harm. To solve the RowHammer problem, our paper examined seven different approaches (including a novel probabilistic approach that has very low cost), some of which influenced or were adopted in different industrial products. Many later works from various research communities examined RowHammer, building real security attacks, proposing new defenses, further analyzing the problem at various (e.g., device/circuit, architecture, and system) levels, and exploiting RowHammer for various purposes (e.g., to reverse-engineer DRAM chips). Industry has worked to mitigate the problem, changing both memory controllers and DRAM standards/chips. Two major DRAM vendors finally wrote papers on the topic in 2023, describing their current approaches to mitigate RowHammer. Research & development on RowHammer in both academia & industry continues to be very active and fascinating. This short retrospective provides a brief analysis of our ISCA 2014 paper and its impact., Comment: Selected to the 50th Anniversary of ISCA (ACM/IEEE International Symposium on Computer Architecture), Commemorative Issue, 2023

Our ISCA 2013 paper provides a fundamental empirical understanding of two major factors that make it very difficult to determine the minimum data retention time of a DRAM cell, based on the first comprehensive experimental characterization of retention time behavior of a large number of modern commodity DRAM chips from 5 major vendors. We study the prevalence, effects, and technology scaling characteristics of two significant phenomena: 1) data pattern dependence (DPD), where the minimum retention time of a DRAM cell is affected by data stored in other DRAM cells, and 2) variable retention time (VRT), where the minimum retention time of a DRAM cell changes unpredictably over time. To this end, we built a flexible FPGA-based testing infrastructure to test DRAM chips, which has enabled a large amount of further experimental research in DRAM. Our ISCA 2013 paper's results using this infrastructure clearly demonstrate that DPD and VRT phenomena are significant issues that must be addressed for correct operation in DRAM-based systems and their effects are getting worse as DRAM scales to smaller technology node sizes. Our work also provides ideas on how to accurately identify data retention times in the presence of DPD and VRT, e.g., online profiling with error correcting codes, which later works examined and enabled. Most modern DRAM chips now incorporate ECC, especially to account for VRT effects. This short retrospective provides a brief analysis of our ISCA 2013 paper and its impact. We describe why we did the work, what we found and its implications, what the findings as well as the infrastructure we built to discover them have enabled in later works, and our thoughts on what the future may bring., Comment: Selected to the 50th Anniversary of ISCA (ACM/IEEE International Symposium on Computer Architecture), Commemorative Issue, 2023

Dynamic Random Access Memory (DRAM) is the prevalent memory technology used to build main memory systems of almost all computers. A fundamental shortcoming of DRAM is the need to refresh memory cells to keep stored data intact. DRAM refresh consumes energy and degrades performance. It is also a technology scaling challenge as its negative effects become worse as DRAM cell size reduces and DRAM chip capacity increases. Our ISCA 2012 paper, RAIDR, examines the DRAM refresh problem from a modern computing systems perspective, demonstrating its projected impact on systems with higher-capacity DRAM chips expected to be manufactured in the future. It proposes and evaluates a simple and low-cost solution that greatly reduces the performance & energy overheads of refresh by exploiting variation in data retention times across DRAM rows. The key idea is to group the DRAM rows into bins in terms of their minimum data retention times, store the bins in low-cost Bloom filters, and refresh rows in different bins at different rates. Evaluations in our paper (and later works) show that the idea greatly improves performance & energy efficiency and its benefits increase with DRAM chip capacity. The paper embodies an approach we have termed system-DRAM co-design. This short retrospective provides a brief analysis of our RAIDR paper and its impact. We briefly describe the mindset and circumstances that led to our focus on the DRAM refresh problem and RAIDR's development, discuss later works that provided improved analyses and solutions, and make some educated guesses on what the future may bring on the DRAM refresh problem (and more generally in DRAM technology scaling)., Comment: Selected to the 50th Anniversary of ISCA (ACM/IEEE International Symposium on Computer Architecture), Commemorative Issue, 2023

Our ISCA 2015 paper provides a new programmable processing-in-memory (PIM) architecture and system design that can accelerate key data-intensive applications, with a focus on graph processing workloads. Our major idea was to completely rethink the system, including the programming model, data partitioning mechanisms, system support, instruction set architecture, along with near-memory execution units and their communication architecture, such that an important workload can be accelerated at a maximum level using a distributed system of well-connected near-memory accelerators. We built our accelerator system, Tesseract, using 3D-stacked memories with logic layers, where each logic layer contains general-purpose processing cores and cores communicate with each other using a message-passing programming model. Cores could be specialized for graph processing (or any other application to be accelerated). To our knowledge, our paper was the first to completely design a near-memory accelerator system from scratch such that it is both generally programmable and specifically customizable to accelerate important applications, with a case study on major graph processing workloads. Ensuing work in academia and industry showed that similar approaches to system design can greatly benefit both graph processing workloads and other applications, such as machine learning, for which ideas from Tesseract seem to have been influential. This short retrospective provides a brief analysis of our ISCA 2015 paper and its impact. We briefly describe the major ideas and contributions of the work, discuss later works that built on it or were influenced by it, and make some educated guesses on what the future may bring on PIM and accelerator systems., Comment: Selected to the 50th Anniversary of ISCA (ACM/IEEE International Symposium on Computer Architecture), Commemorative Issue, 2023

Memory-centric computing aims to enable computation capability in and near all places where data is generated and stored. As such, it can greatly reduce the large negative performance and energy impact of data access and data movement, by fundamentally avoiding data movement and reducing data access latency & energy. Many recent studies show that memory-centric computing can greatly improve system performance and energy efficiency. Major industrial vendors and startup companies have also recently introduced memory chips that have sophisticated computation capabilities. This talk describes promising ongoing research and development efforts in memory-centric computing. We classify such efforts into two major fundamental categories: 1) processing using memory, which exploits analog operational properties of memory structures to perform massively-parallel operations in memory, and 2) processing near memory, which integrates processing capability in memory controllers, the logic layer of 3D-stacked memory technologies, or memory chips to enable high-bandwidth and low-latency memory access to near-memory logic. We show both types of architectures (and their combination) can enable orders of magnitude improvements in performance and energy consumption of many important workloads, such as graph analytics, databases, machine learning, video processing, climate modeling, genome analysis. We discuss adoption challenges for the memory-centric computing paradigm and conclude with some research & development opportunities., Comment: To appear as an invited special session paper at DAC 2023